From 0ecfcabe4e0991148383fa32cb444020643a2cdc Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 23 Aug 2024 10:50:01 +0200 Subject: [PATCH 01/49] bump to 1.8.0dev --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 603d9091..d81496f4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -314,7 +314,7 @@ manifest { description = """A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data""" mainScript = 'main.nf' nextflowVersion = '!>=23.10.0' - version = '1.7.0' + version = '1.8.0dev' doi = '' } From 0754de2df80bc6d4261555547f5e58ffc871ef1c Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 28 Aug 2024 14:31:45 +0200 Subject: [PATCH 02/49] first batch of updates --- main.nf | 269 +++++++++--------- modules.json | 8 +- nextflow.config | 7 + nextflow_schema.json | 6 + .../utils_cmgg_germline_pipeline/main.nf | 62 ++-- .../nf-core/utils_nextflow_pipeline/main.nf | 24 +- .../tests/nextflow.config | 2 +- .../nf-core/utils_nfcore_pipeline/main.nf | 45 ++- .../nf-core/utils_nfschema_plugin/main.nf | 46 +++ .../nf-core/utils_nfschema_plugin/meta.yml | 35 +++ .../utils_nfschema_plugin/tests/main.nf.test | 117 ++++++++ .../tests/nextflow.config | 8 + .../tests/nextflow_schema.json | 8 +- .../nf-core/utils_nfvalidation_plugin/main.nf | 62 ---- .../utils_nfvalidation_plugin/meta.yml | 44 --- .../tests/main.nf.test | 200 ------------- .../utils_nfvalidation_plugin/tests/tags.yml | 2 - 17 files changed, 428 insertions(+), 517 deletions(-) create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/main.nf create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/meta.yml create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config rename subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/nextflow_schema.json (95%) delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml diff --git a/main.nf b/main.nf index 16f7ecf8..28f4bd0e 100644 --- a/main.nf +++ b/main.nf @@ -7,87 +7,36 @@ ---------------------------------------------------------------------------------------- */ -nextflow.enable.dsl = 2 - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { getGenomeAttribute } from './subworkflows/local/utils_cmgg_germline_pipeline' - -params.fasta = getGenomeAttribute('fasta') -params.fai = getGenomeAttribute('fai') -params.dict = getGenomeAttribute('dict') -params.strtablefile = getGenomeAttribute('strtablefile') -params.sdf = getGenomeAttribute('sdf') -params.dbsnp = getGenomeAttribute('dbsnp') -params.dbsnp_tbi = getGenomeAttribute('dbsnp_tbi') -params.vep_cache = getGenomeAttribute('vep_cache') -params.dbnsfp = getGenomeAttribute('dbnsfp') -params.dbnsfp_tbi = getGenomeAttribute('dbnsfp_tbi') -params.spliceai_indel = getGenomeAttribute('spliceai_indel') -params.spliceai_indel_tbi = getGenomeAttribute('spliceai_indel_tbi') -params.spliceai_snv = getGenomeAttribute('spliceai_snv') -params.spliceai_snv_tbi = getGenomeAttribute('spliceai_snv_tbi') -params.mastermind = getGenomeAttribute('mastermind') -params.mastermind_tbi = getGenomeAttribute('mastermind_tbi') -params.eog = getGenomeAttribute('eog') -params.eog_tbi = getGenomeAttribute('eog_tbi') -params.alphamissense = getGenomeAttribute('alphamissense') -params.alphamissense_tbi = getGenomeAttribute('alphamissense_tbi') -params.vcfanno_resources = getGenomeAttribute('vcfanno_resources') -params.vcfanno_config = getGenomeAttribute('vcfanno_config') - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - VALIDATE INPUTS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// Check for dependencies between parameters -// - -if(params.dbsnp_tbi && !params.dbsnp){ - error("Please specify the dbsnp VCF with --dbsnp VCF") -} - -if (params.annotate) { - // Check if a genome is given - if (!params.genome) { error("A genome should be supplied for annotation (use --genome)") } - - // Check if the VEP versions were given - if (!params.vep_version) { error("A VEP version should be supplied for annotation (use --vep_version)") } - if (!params.vep_cache_version) { error("A VEP cache version should be supplied for annotation (use --vep_cache_version)") } - - // Check if a species is entered - if (!params.species) { error("A species should be supplied for annotation (use --species)") } - - // Check if all vcfanno files are supplied when vcfanno should be used - if (params.vcfanno && (!params.vcfanno_config || !params.vcfanno_resources)) { - error("A TOML file and resource files should be supplied when using vcfanno (use --vcfanno_config and --vcfanno_resources)") - } -} - -callers = params.callers.tokenize(",") -for(caller in callers) { - if(!(caller in GlobalVariables.availableCallers)) { error("\"${caller}\" is not a supported callers please use one or more of these instead: ${GlobalVariables.availableCallers}")} -} - -if (params.output_suffix && callers.size() > 1) { - error("Cannot use --output_suffix with more than one caller") -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CONFIG FILES -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -multiqc_logo = params.multiqc_logo ?: "$projectDir/assets/CMGG_logo.png" - +include { getGenomeAttribute } from './subworkflows/local/utils_cmgg_germline_pipeline' + +params.fasta = getGenomeAttribute('fasta', params.genomes, params.genome) +params.fai = getGenomeAttribute('fai', params.genomes, params.genome) +params.dict = getGenomeAttribute('dict', params.genomes, params.genome) +params.strtablefile = getGenomeAttribute('strtablefile', params.genomes, params.genome) +params.sdf = getGenomeAttribute('sdf', params.genomes, params.genome) +params.dbsnp = getGenomeAttribute('dbsnp', params.genomes, params.genome) +params.dbsnp_tbi = getGenomeAttribute('dbsnp_tbi', params.genomes, params.genome) +params.vep_cache = getGenomeAttribute('vep_cache', params.genomes, params.genome) +params.dbnsfp = getGenomeAttribute('dbnsfp', params.genomes, params.genome) +params.dbnsfp_tbi = getGenomeAttribute('dbnsfp_tbi', params.genomes, params.genome) +params.spliceai_indel = getGenomeAttribute('spliceai_indel', params.genomes, params.genome) +params.spliceai_indel_tbi = getGenomeAttribute('spliceai_indel_tbi', params.genomes, params.genome) +params.spliceai_snv = getGenomeAttribute('spliceai_snv', params.genomes, params.genome) +params.spliceai_snv_tbi = getGenomeAttribute('spliceai_snv_tbi', params.genomes, params.genome) +params.mastermind = getGenomeAttribute('mastermind', params.genomes, params.genome) +params.mastermind_tbi = getGenomeAttribute('mastermind_tbi', params.genomes, params.genome) +params.eog = getGenomeAttribute('eog', params.genomes, params.genome) +params.eog_tbi = getGenomeAttribute('eog_tbi', params.genomes, params.genome) +params.alphamissense = getGenomeAttribute('alphamissense', params.genomes, params.genome) +params.alphamissense_tbi = getGenomeAttribute('alphamissense_tbi', params.genomes, params.genome) +params.vcfanno_resources = getGenomeAttribute('vcfanno_resources', params.genomes, params.genome) +params.vcfanno_config = getGenomeAttribute('vcfanno_config', params.genomes, params.genome) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -106,7 +55,9 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_cmgg_germli workflow NFCMGG_GERMLINE { take: - samplesheet // channel: samplesheet read in from --input + samplesheet // channel: samplesheet read in from --input + pipeline_params // the parameters used for this pipeline + multiqc_logo // string: the path to the multiqc logo main: @@ -118,66 +69,66 @@ workflow NFCMGG_GERMLINE { samplesheet, // File inputs - params.fasta, - params.fai, - params.dict, - params.strtablefile, - params.sdf, - params.dbsnp, - params.dbsnp_tbi, - params.vep_cache, - params.dbnsfp, - params.dbnsfp_tbi, - params.spliceai_indel, - params.spliceai_indel_tbi, - params.spliceai_snv, - params.spliceai_snv_tbi, - params.mastermind, - params.mastermind_tbi, - params.eog, - params.eog_tbi, - params.alphamissense, - params.alphamissense_tbi, - params.vcfanno_resources, - params.vcfanno_config, - params.multiqc_config, + pipeline_params.fasta, + pipeline_params.fai, + pipeline_params.dict, + pipeline_params.strtablefile, + pipeline_params.sdf, + pipeline_params.dbsnp, + pipeline_params.dbsnp_tbi, + pipeline_params.vep_cache, + pipeline_params.dbnsfp, + pipeline_params.dbnsfp_tbi, + pipeline_params.spliceai_indel, + pipeline_params.spliceai_indel_tbi, + pipeline_params.spliceai_snv, + pipeline_params.spliceai_snv_tbi, + pipeline_params.mastermind, + pipeline_params.mastermind_tbi, + pipeline_params.eog, + pipeline_params.eog_tbi, + pipeline_params.alphamissense, + pipeline_params.alphamissense_tbi, + pipeline_params.vcfanno_resources, + pipeline_params.vcfanno_config, + pipeline_params.multiqc_config, multiqc_logo, - params.multiqc_methods_description, - params.roi, - params.somalier_sites, - params.vcfanno_lua, - params.updio_common_cnvs, - params.automap_repeats, - params.automap_panel, - params.outdir, + pipeline_params.multiqc_methods_description, + pipeline_params.roi, + pipeline_params.somalier_sites, + pipeline_params.vcfanno_lua, + pipeline_params.updio_common_cnvs, + pipeline_params.automap_repeats, + pipeline_params.automap_panel, + pipeline_params.outdir, GlobalVariables.pedFiles, // Boolean inputs - params.dragstr, - params.annotate, - params.vcfanno, - params.only_call, - params.only_merge, - params.filter, - params.normalize, - params.add_ped, - params.gemini, - params.validate, - params.updio, - params.automap, - params.vep_dbnsfp, - params.vep_spliceai, - params.vep_mastermind, - params.vep_eog, - params.vep_alphamissense, + pipeline_params.dragstr, + pipeline_params.annotate, + pipeline_params.vcfanno, + pipeline_params.only_call, + pipeline_params.only_merge, + pipeline_params.filter, + pipeline_params.normalize, + pipeline_params.add_ped, + pipeline_params.gemini, + pipeline_params.validate, + pipeline_params.updio, + pipeline_params.automap, + pipeline_params.vep_dbnsfp, + pipeline_params.vep_spliceai, + pipeline_params.vep_mastermind, + pipeline_params.vep_eog, + pipeline_params.vep_alphamissense, // Value inputs - params.genome, - params.species, - params.vep_cache_version, - params.vep_chunk_size, - params.scatter_count, - params.callers.tokenize(",") + pipeline_params.genome, + pipeline_params.species, + pipeline_params.vep_cache_version, + pipeline_params.vep_chunk_size, + pipeline_params.scatter_count, + pipeline_params.callers.tokenize(",") ) emit: @@ -195,6 +146,55 @@ workflow { main: + /* + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + VALIDATE INPUTS + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + */ + + // + // Check for dependencies between parameters + // + + if(params.dbsnp_tbi && !params.dbsnp){ + error("Please specify the dbsnp VCF with --dbsnp VCF") + } + + if (params.annotate) { + // Check if a genome is given + if (!params.genome) { error("A genome should be supplied for annotation (use --genome)") } + + // Check if the VEP versions were given + if (!params.vep_version) { error("A VEP version should be supplied for annotation (use --vep_version)") } + if (!params.vep_cache_version) { error("A VEP cache version should be supplied for annotation (use --vep_cache_version)") } + + // Check if a species is entered + if (!params.species) { error("A species should be supplied for annotation (use --species)") } + + // Check if all vcfanno files are supplied when vcfanno should be used + if (params.vcfanno && (!params.vcfanno_config || !params.vcfanno_resources)) { + error("A TOML file and resource files should be supplied when using vcfanno (use --vcfanno_config and --vcfanno_resources)") + } + } + + callers = params.callers.tokenize(",") + callers.each { caller -> + if(!(caller in GlobalVariables.availableCallers)) { error("\"${caller}\" is not a supported callers please use one or more of these instead: ${GlobalVariables.availableCallers}")} + } + + if (params.output_suffix && callers.size() > 1) { + error("Cannot use --output_suffix with more than one caller") + } + + /* + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CONFIG FILES + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + */ + + def multiqc_logo = params.multiqc_logo ?: "$projectDir/assets/CMGG_logo.png" + + // // SUBWORKFLOW: Run initialisation tasks // @@ -205,14 +205,19 @@ workflow { params.monochrome_logs, args, params.outdir, - params.input + params.input, + params.ped, + params.genomes, + params.genome ) // // WORKFLOW: Run main workflow // NFCMGG_GERMLINE ( - PIPELINE_INITIALISATION.out.samplesheet + PIPELINE_INITIALISATION.out.samplesheet, + params, + multiqc_logo ) // diff --git a/modules.json b/modules.json index 6f8e48ba..e9fc85b7 100644 --- a/modules.json +++ b/modules.json @@ -232,17 +232,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8", + "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", "installed_by": ["subworkflows"] }, - "utils_nfvalidation_plugin": { + "utils_nfschema_plugin": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", "installed_by": ["subworkflows"] }, "vcf_annotate_ensemblvep_snpeff": { diff --git a/nextflow.config b/nextflow.config index d81496f4..807afbb9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -80,6 +80,7 @@ params { igenomes_base = null //'s3://ngi-igenomes/igenomes' igenomes_ignore = true genome = "GRCh38" + genomes = [:] genomes_base = "/references/" genomes_ignore = false @@ -262,6 +263,12 @@ validation { lenientMode = false defaultIgnoreParams = ['genomes','igenomes_base','test_data'] showHiddenParams = false + help { + enabled = true + //beforeText = TODO + //afterText = TODO + command = "nextflow run nf-cmgg/germline -profile docker --input --outdir " + } } // Load igenomes.config if required diff --git a/nextflow_schema.json b/nextflow_schema.json index fb6d0551..aa86f2d4 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -128,6 +128,12 @@ "hidden": true, "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.", "default": true + }, + "genomes": { + "type": "object", + "description": "A map structure containing the paths to all genome references", + "hidden": true, + "default": {} } }, "required": ["fasta"] diff --git a/subworkflows/local/utils_cmgg_germline_pipeline/main.nf b/subworkflows/local/utils_cmgg_germline_pipeline/main.nf index 232d17b5..a07a7d45 100644 --- a/subworkflows/local/utils_cmgg_germline_pipeline/main.nf +++ b/subworkflows/local/utils_cmgg_germline_pipeline/main.nf @@ -8,17 +8,14 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' include { paramsSummaryMap } from 'plugin/nf-schema' include { samplesheetToList } from 'plugin/nf-schema' include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' -include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' /* ======================================================================================== @@ -36,6 +33,9 @@ workflow PIPELINE_INITIALISATION { nextflow_cli_args // array: List of positional nextflow CLI args outdir // string: The output directory where the results will be saved input // string: Path to input samplesheet + pedFile // string: Path to the common PED file + genomesMap // map: A map structure containing the references for each genome + genome // string: The genome to use main: @@ -54,16 +54,10 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // - pre_help_text = nfCoreLogo(monochrome_logs) - post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) - def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " - UTILS_NFVALIDATION_PLUGIN ( - help, - workflow_command, - pre_help_text, - post_help_text, + UTILS_NFSCHEMA_PLUGIN ( + workflow, validate_params, - "nextflow_schema.json" + null ) // @@ -75,20 +69,20 @@ workflow PIPELINE_INITIALISATION { // // Custom validation for pipeline parameters // - validateInputParameters() + validateInputParameters(genomesMap, genome) // // Create channel from input file provided through params.input // // Output the samplesheet - file(params.input).copyTo("${params.outdir}/samplesheet.csv") + file(input).copyTo("${outdir}/samplesheet.csv") - def Pedigree pedigree = new Pedigree(params.ped) + def pedigree = new Pedigree(pedFile) - def List samplesheetList = samplesheetToList(params.input, "assets/schema_input.json") - samplesheetList.each { - ped = it[6] + def samplesheetList = samplesheetToList(input, "assets/schema_input.json") + samplesheetList.each { row -> + def ped = row[6] if(ped) { pedigree.addPedContent(ped) } } GlobalVariables.pedFiles = pedigree.writePeds(workflow) @@ -103,7 +97,9 @@ workflow PIPELINE_INITIALISATION { [ new_meta, cram, crai, gvcf, tbi, roi, truth_vcf, truth_tbi, truth_bed ] } .tap { ch_raw_inputs } - .map { [ "id":it[0].id, "family":it[0].family ] } + .map { row -> + [ "id":row[0].id, "family":row[0].family ] + } .reduce([:]) { families, v -> // Count the unique samples in one family families[v.family] = families[v.family] ? families[v.family] + [v.id] : [v.id] @@ -167,17 +163,17 @@ workflow PIPELINE_COMPLETION { // // Check and validate pipeline parameters // -def validateInputParameters() { - genomeExistsError() +def validateInputParameters(genomesMap, genome) { + genomeExistsError(genomesMap, genome) } // // Get attribute from genome config file e.g. fasta // -def getGenomeAttribute(attribute) { - if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { - if (params.genomes[ params.genome ].containsKey(attribute)) { - return params.genomes[ params.genome ][ attribute ] +def getGenomeAttribute(attribute, genomesMap, genome) { + if (genomesMap && genome && genomesMap.containsKey(genome)) { + if (genomesMap[ genome ].containsKey(attribute)) { + return genomesMap[ genome ][ attribute ] } } return null @@ -186,12 +182,12 @@ def getGenomeAttribute(attribute) { // // Exit pipeline if incorrect --genome key provided // -def genomeExistsError() { - if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { +def genomeExistsError(genomesMap, genome) { + if (genomesMap && genome && !genomesMap.containsKey(genome)) { def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + + " Genome '${genome}' not found in any config files provided to the pipeline.\n" + " Currently, the available genome keys are:\n" + - " ${params.genomes.keySet().join(", ")}\n" + + " ${genomesMap.keySet().join(", ")}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" error(error_string) } @@ -231,8 +227,10 @@ def methodsDescriptionText(mqc_methods_yaml) { // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list def temp_doi_ref = "" - String[] manifest_doi = meta.manifest_map.doi.tokenize(",") - for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + def manifest_doi = meta.manifest_map.doi.tokenize(",") + manifest_doi.each { doi_ref -> + temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + } meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) } else meta["doi_text"] = "" meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index ac31f28f..28e32b20 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -2,10 +2,6 @@ // Subworkflow with functionality that may be useful for any Nextflow pipeline // -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - /* ======================================================================================== SUBWORKFLOW DEFINITION @@ -58,7 +54,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Generate version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -79,10 +75,10 @@ def dumpParametersToJSON(outdir) { def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') def filename = "params_${timestamp}.json" def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) - FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() } @@ -90,7 +86,7 @@ def dumpParametersToJSON(outdir) { // When running with -profile conda, warn if channels have not been set-up appropriately // def checkCondaChannels() { - Yaml parser = new Yaml() + def parser = new org.yaml.snakeyaml.Yaml() def channels = [] try { def config = parser.load("conda config --show channels".execute().text) @@ -102,14 +98,16 @@ def checkCondaChannels() { // Check that all channels are present // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def required_channels_in_order = ['conda-forge', 'bioconda'] def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + + required_channels_in_order.eachWithIndex { channel, index -> + if (index < required_channels_in_order.size() - 1) { + channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1])) + } } if (channels_missing | channel_priority_violation) { diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index d0a926bf..a09572e5 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -3,7 +3,7 @@ manifest { author = """nf-core""" homePage = 'https://127.0.0.1' description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 14558c39..cbd8495b 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -2,9 +2,6 @@ // Subworkflow with utility functions specific to the nf-core pipeline template // -import org.yaml.snakeyaml.Yaml -import nextflow.extension.FilesEx - /* ======================================================================================== SUBWORKFLOW DEFINITION @@ -34,7 +31,7 @@ workflow UTILS_NFCORE_PIPELINE { // Warn if a -profile or Nextflow config has not been provided to run the pipeline // def checkConfigProvided() { - valid_config = true + def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + @@ -66,11 +63,13 @@ def checkProfileProvided(nextflow_cli_args) { // def workflowCitation() { def temp_doi_ref = "" - String[] manifest_doi = workflow.manifest.doi.tokenize(",") + def manifest_doi = workflow.manifest.doi.tokenize(",") // Using a loop to handle multiple DOIs // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list - for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" + manifest_doi.each { doi_ref -> + temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" + } return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + @@ -84,7 +83,7 @@ def workflowCitation() { // Generate workflow version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -102,8 +101,8 @@ def getWorkflowVersion() { // Get software versions for pipeline // def processVersionsFromYAML(yaml_file) { - Yaml yaml = new Yaml() - versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def yaml = new org.yaml.snakeyaml.Yaml() + def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } return yaml.dumpAsMap(versions).trim() } @@ -124,7 +123,7 @@ def workflowVersionToYAML() { def softwareVersionsToYAML(ch_versions) { return ch_versions .unique() - .map { processVersionsFromYAML(it) } + .map { version -> processVersionsFromYAML(version) } .unique() .mix(Channel.of(workflowVersionToYAML())) } @@ -134,19 +133,19 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - for (group in summary_params.keySet()) { + summary_params.keySet().each { group -> def group_params = summary_params.get(group) // This gets the parameters of that particular group if (group_params) { summary_section += "

    $group

    \n" summary_section += "
    \n" - for (param in group_params.keySet()) { + group_params.keySet().sort().each { param -> summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" } summary_section += "
    \n" } } - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" @@ -161,7 +160,7 @@ def paramsSummaryMultiqc(summary_params) { // nf-core logo // def nfCoreLogo(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map String.format( """\n ${dashedLine(monochrome_logs)} @@ -180,7 +179,7 @@ def nfCoreLogo(monochrome_logs=true) { // Return dashed line // def dashedLine(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map return "-${colors.dim}----------------------------------------------------${colors.reset}-" } @@ -188,7 +187,7 @@ def dashedLine(monochrome_logs=true) { // ANSII colours used for terminal logging // def logColours(monochrome_logs=true) { - Map colorcodes = [:] + def colorcodes = [:] as Map // Reset / Meta colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" @@ -287,7 +286,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi } def summary = [:] - for (group in summary_params.keySet()) { + summary_params.keySet().sort().each { group -> summary << summary_params[group] } @@ -344,10 +343,10 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def sendmail_html = sendmail_template.toString() // Send the HTML e-mail - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } @@ -364,13 +363,13 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); output_tf.delete() } @@ -378,7 +377,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Print pipeline summary on completion // def completionSummary(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" @@ -395,7 +394,7 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] - for (group in summary_params.keySet()) { + summary_params.keySet().sort().each { group -> summary << summary_params[group] } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf new file mode 100644 index 00000000..4994303e --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -0,0 +1,46 @@ +// +// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary +// + +include { paramsSummaryLog } from 'plugin/nf-schema' +include { validateParameters } from 'plugin/nf-schema' + +workflow UTILS_NFSCHEMA_PLUGIN { + + take: + input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow + validate_params // boolean: validate the parameters + parameters_schema // string: path to the parameters JSON schema. + // this has to be the same as the schema given to `validation.parametersSchema` + // when this input is empty it will automatically use the configured schema or + // "${projectDir}/nextflow_schema.json" as default. This input should not be empty + // for meta pipelines + + main: + + // + // Print parameter summary to stdout. This will display the parameters + // that differ from the default given in the JSON schema + // + if(parameters_schema) { + log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) + } else { + log.info paramsSummaryLog(input_workflow) + } + + // + // Validate the parameters using nextflow_schema.json or the schema + // given via the validation.parametersSchema configuration option + // + if(validate_params) { + if(parameters_schema) { + validateParameters(parameters_schema:parameters_schema) + } else { + validateParameters() + } + } + + emit: + dummy_emit = true +} + diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml new file mode 100644 index 00000000..f7d9f028 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -0,0 +1,35 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "utils_nfschema_plugin" +description: Run nf-schema to validate parameters and create a summary of changed parameters +keywords: + - validation + - JSON schema + - plugin + - parameters + - summary +components: [] +input: + - input_workflow: + type: object + description: | + The workflow object of the used pipeline. + This object contains meta data used to create the params summary log + - validate_params: + type: boolean + description: Validate the parameters and error if invalid. + - parameters_schema: + type: string + description: | + Path to the parameters JSON schema. + This has to be the same as the schema given to the `validation.parametersSchema` config + option. When this input is empty it will automatically use the configured schema or + "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way + for meta pipelines. +output: + - dummy_emit: + type: boolean + description: Dummy emit to make nf-core subworkflows lint happy +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test new file mode 100644 index 00000000..842dc432 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -0,0 +1,117 @@ +nextflow_workflow { + + name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" + script "../main.nf" + workflow "UTILS_NFSCHEMA_PLUGIN" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/utils_nfschema_plugin" + tag "plugin/nf-schema" + + config "./nextflow.config" + + test("Should run nothing") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } + + test("Should run nothing - custom schema") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params - custom schema") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config new file mode 100644 index 00000000..0907ac58 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -0,0 +1,8 @@ +plugins { + id "nf-schema@2.1.0" +} + +validation { + parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + monochromeLogs = true +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json similarity index 95% rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json index 7626c1c9..331e0d2f 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", "title": ". pipeline parameters", "description": "", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -87,10 +87,10 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf deleted file mode 100644 index 50155c08..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf +++ /dev/null @@ -1,62 +0,0 @@ -// -// Subworkflow that uses the nf-validation plugin to render help text and parameter summary -// - -/* -======================================================================================== - IMPORT NF-VALIDATION PLUGIN -======================================================================================== -*/ - -include { paramsHelp } from 'plugin/nf-schema' -include { paramsSummaryLog } from 'plugin/nf-schema' -include { validateParameters } from 'plugin/nf-schema' - -/* -======================================================================================== - SUBWORKFLOW DEFINITION -======================================================================================== -*/ - -workflow UTILS_NFVALIDATION_PLUGIN { - - take: - print_help // boolean: print help - workflow_command // string: default commmand used to run pipeline - pre_help_text // string: string to be printed before help text and summary log - post_help_text // string: string to be printed after help text and summary log - validate_params // boolean: validate parameters - schema_filename // path: JSON schema file, null to use default value - - main: - - log.debug "Using schema file: ${schema_filename}" - - // Default values for strings - pre_help_text = pre_help_text ?: '' - post_help_text = post_help_text ?: '' - workflow_command = workflow_command ?: '' - - // - // Print help message if needed - // - if (print_help) { - log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text - System.exit(0) - } - - // - // Print parameter summary to stdout - // - log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text - - // - // Validate parameters relative to the parameter JSON schema - // - if (validate_params){ - validateParameters(parameters_schema: schema_filename) - } - - emit: - dummy_emit = true -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml deleted file mode 100644 index 3d4a6b04..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml +++ /dev/null @@ -1,44 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "UTILS_NFVALIDATION_PLUGIN" -description: Use nf-validation to initiate and validate a pipeline -keywords: - - utility - - pipeline - - initialise - - validation -components: [] -input: - - print_help: - type: boolean - description: | - Print help message and exit - - workflow_command: - type: string - description: | - The command to run the workflow e.g. "nextflow run main.nf" - - pre_help_text: - type: string - description: | - Text to print before the help message - - post_help_text: - type: string - description: | - Text to print after the help message - - validate_params: - type: boolean - description: | - Validate the parameters and error if invalid. - - schema_filename: - type: string - description: | - The filename of the schema to validate against. -output: - - dummy_emit: - type: boolean - description: | - Dummy emit to make nf-core subworkflows lint happy -authors: - - "@adamrtalbot" -maintainers: - - "@adamrtalbot" - - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test deleted file mode 100644 index 5784a33f..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ /dev/null @@ -1,200 +0,0 @@ -nextflow_workflow { - - name "Test Workflow UTILS_NFVALIDATION_PLUGIN" - script "../main.nf" - workflow "UTILS_NFVALIDATION_PLUGIN" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "plugin/nf-validation" - tag "'plugin/nf-validation'" - tag "utils_nfvalidation_plugin" - tag "subworkflows/utils_nfvalidation_plugin" - - test("Should run nothing") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should run help") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with command") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with extra text") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = "pre-help-text" - post_help_text = "post-help-text" - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('pre-help-text') } }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } }, - { assert workflow.stdout.any { it.contains('post-help-text') } } - ) - } - } - - test("Should validate params") { - - when { - - params { - monochrome_logs = true - test_data = '' - outdir = 1 - } - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = true - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } - ) - } - } -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml deleted file mode 100644 index 60b1cfff..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfvalidation_plugin: - - subworkflows/nf-core/utils_nfvalidation_plugin/** From fe7cfad4e2984a6e05a179f56abe4bd0a0f0c136 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 28 Aug 2024 14:58:24 +0200 Subject: [PATCH 03/49] second batch of updates --- main.nf | 2 +- subworkflows/local/cram_call_gatk4/main.nf | 18 +++++++------ .../local/cram_call_vardictjava/main.nf | 3 ++- .../cram_prepare_samtools_bedtools/main.nf | 25 ++++++++++--------- .../local/gvcf_joint_genotype_gatk4/main.nf | 10 ++++---- .../utils_cmgg_germline_pipeline/main.nf | 5 ++-- .../local/vcf_concat_bcftools/main.nf | 1 + .../local/vcf_filter_bcftools/main.nf | 1 + subworkflows/local/vcf_roh_automap/main.nf | 1 + subworkflows/local/vcf_upd_updio/main.nf | 12 ++++++--- 10 files changed, 46 insertions(+), 32 deletions(-) diff --git a/main.nf b/main.nf index 28f4bd0e..b64b8d83 100644 --- a/main.nf +++ b/main.nf @@ -192,7 +192,7 @@ workflow { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - def multiqc_logo = params.multiqc_logo ?: "$projectDir/assets/CMGG_logo.png" + def multiqc_logo = params.multiqc_logo ?: "$projectDir/assets/CMGG_logo.png" // diff --git a/subworkflows/local/cram_call_gatk4/main.nf b/subworkflows/local/cram_call_gatk4/main.nf index 475903d9..308b69f0 100644 --- a/subworkflows/local/cram_call_gatk4/main.nf +++ b/subworkflows/local/cram_call_gatk4/main.nf @@ -27,6 +27,7 @@ workflow CRAM_CALL_GATK4 { // Generate DRAGSTR models (if --dragstr is specified) // + ch_cram_models = Channel.empty() if (dragstr) { ch_input @@ -43,10 +44,10 @@ workflow CRAM_CALL_GATK4 { GATK4_CALIBRATEDRAGSTRMODEL( ch_dragstr_input.map { meta, cram, crai, beds -> [ meta, cram, crai ] }, - ch_fasta.map { it[1] }, - ch_fai.map { it[1] }, - ch_dict.map { it[1] }, - ch_strtablefile.map { it[1] } + ch_fasta.map { meta, fasta -> fasta }, + ch_fai.map { meta, fai -> fai }, + ch_dict.map { meta, dict -> dict }, + ch_strtablefile.map { meta, str -> str } ) ch_versions = ch_versions.mix(GATK4_CALIBRATEDRAGSTRMODEL.out.versions.first()) @@ -98,10 +99,11 @@ workflow CRAM_CALL_GATK4 { ) ch_versions = ch_versions.mix(BCFTOOLS_STATS_SINGLE.out.versions.first()) - emit: - gvcfs = VCF_CONCAT_BCFTOOLS.out.vcfs // channel: [ val(meta), path(vcf), path(tbi) ] + reports = BCFTOOLS_STATS_SINGLE.out.stats.collect{ meta, report -> report} - reports = BCFTOOLS_STATS_SINGLE.out.stats.collect{it[1]} // channel: [ path(stats) ] - versions = ch_versions // channel: [ versions.yml ] + emit: + gvcfs = VCF_CONCAT_BCFTOOLS.out.vcfs // channel: [ val(meta), path(vcf), path(tbi) ] + reports // channel: [ path(stats) ] + versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/local/cram_call_vardictjava/main.nf b/subworkflows/local/cram_call_vardictjava/main.nf index c75a4495..0475d947 100644 --- a/subworkflows/local/cram_call_vardictjava/main.nf +++ b/subworkflows/local/cram_call_vardictjava/main.nf @@ -78,9 +78,10 @@ workflow CRAM_CALL_VARDICTJAVA { ) ch_versions = ch_versions.mix(VCF_CONCAT_BCFTOOLS.out.versions) + ch_dbsnp_annotated = Channel.empty() if(ch_dbsnp) { ch_dbsnp - .map { [ get_vcfanno_config(it[0]) ] } + .map { meta, dbsnp -> [ get_vcfanno_config(dbsnp) ] } .collect() .set { ch_vcfanno_toml } diff --git a/subworkflows/local/cram_prepare_samtools_bedtools/main.nf b/subworkflows/local/cram_prepare_samtools_bedtools/main.nf index 32353a29..b18f003b 100644 --- a/subworkflows/local/cram_prepare_samtools_bedtools/main.nf +++ b/subworkflows/local/cram_prepare_samtools_bedtools/main.nf @@ -32,14 +32,12 @@ workflow CRAM_PREPARE_SAMTOOLS_BEDTOOLS { ch_crams .groupTuple() // No size needed here because this runs before any process - .branch( - { meta, cram, crai -> - multiple: cram.size() > 1 - return [meta, cram] - single: cram.size() == 1 - return [meta, cram[0], crai[0]] - } - ) + .branch { meta, cram, crai -> + multiple: cram.size() > 1 + return [meta, cram] + single: cram.size() == 1 + return [meta, cram[0], crai[0]] + } .set { ch_cram_branch } ch_cram_branch.multiple.dump(tag:'cram_branch_multiple', pretty:true) @@ -93,11 +91,11 @@ workflow CRAM_PREPARE_SAMTOOLS_BEDTOOLS { // sample contains an ROI file def is_present = false def output_roi = [] - for( entry : roi) { + roi.each { entry -> if(entry != []){ output_roi.add(entry) is_present = true - } + } } found: is_present return [ meta, output_roi ] @@ -114,16 +112,19 @@ workflow CRAM_PREPARE_SAMTOOLS_BEDTOOLS { // Add the default ROI file to all samples without an ROI file // if an ROI BED file has been given through the --roi parameter + ch_missing_rois = Channel.empty() if (ch_default_roi) { MERGE_ROI_PARAMS( - ch_default_roi.map { [[id:"default_roi"], it]}, + ch_default_roi.map { bed -> + [[id:"default_roi"], bed] + }, ch_fai ) ch_versions = ch_versions.mix(MERGE_ROI_PARAMS.out.versions) ch_roi_branch.missing .groupTuple() // A specified size isn't needed here since this runs before any process using the default ROI file is executed - .combine(MERGE_ROI_PARAMS.out.bed.map { it[1] }) + .combine(MERGE_ROI_PARAMS.out.bed.map { meta, bed -> bed }) .map { meta, missing, default_roi -> [ meta, default_roi ] } diff --git a/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf b/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf index d2aa1d96..cf7934a4 100644 --- a/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf +++ b/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf @@ -60,7 +60,7 @@ workflow GVCF_JOINT_GENOTYPE_GATK4 { def new_meta = meta + [samples: "${samples.sort(false).join(',')}"] // Having a comma-separated string ensures that joins don't fail [ new_meta, gvcf, tbi ] } - .combine(GAWK.out.output.map { it[1] }) + .combine(GAWK.out.output.map { meta, bed -> bed }) .map { meta, gvcfs, tbis, bed -> [ meta, gvcfs, tbis, bed, [], [] ] } @@ -116,7 +116,7 @@ workflow GVCF_JOINT_GENOTYPE_GATK4 { INPUT_SPLIT_BEDTOOLS( MERGE_BEDS.out.bed.map { meta, bed -> // Multiply the scatter count by the family size to better scatter big families - [meta, bed, (params.scatter_count * meta.family_count)] + [meta, bed, (scatter_count * meta.family_count)] }, GATK4_GENOMICSDBIMPORT.out.genomicsdb.map { meta, genomicsdb -> [ meta, genomicsdb, [] ]} ) @@ -134,9 +134,9 @@ workflow GVCF_JOINT_GENOTYPE_GATK4 { GATK4_GENOTYPEGVCFS( ch_genotypegvcfs_input, - ch_fasta.map { it[1] }, - ch_fai.map { it[1] }, - ch_dict.map { it[1] }, + ch_fasta.map { meta, fasta -> fasta }, + ch_fai.map { meta, fai -> fai }, + ch_dict.map { meta, dict -> dict }, ch_dbsnp, ch_dbsnp_tbi ) diff --git a/subworkflows/local/utils_cmgg_germline_pipeline/main.nf b/subworkflows/local/utils_cmgg_germline_pipeline/main.nf index a07a7d45..f70e310a 100644 --- a/subworkflows/local/utils_cmgg_germline_pipeline/main.nf +++ b/subworkflows/local/utils_cmgg_germline_pipeline/main.nf @@ -76,11 +76,12 @@ workflow PIPELINE_INITIALISATION { // // Output the samplesheet - file(input).copyTo("${outdir}/samplesheet.csv") + def input_file = file(input) + input_file.copyTo("${outdir}/samplesheet.csv") def pedigree = new Pedigree(pedFile) - def samplesheetList = samplesheetToList(input, "assets/schema_input.json") + def samplesheetList = samplesheetToList(input_file, "assets/schema_input.json") samplesheetList.each { row -> def ped = row[6] if(ped) { pedigree.addPedContent(ped) } diff --git a/subworkflows/local/vcf_concat_bcftools/main.nf b/subworkflows/local/vcf_concat_bcftools/main.nf index 47fdc8cb..c88aebe8 100644 --- a/subworkflows/local/vcf_concat_bcftools/main.nf +++ b/subworkflows/local/vcf_concat_bcftools/main.nf @@ -27,6 +27,7 @@ workflow VCF_CONCAT_BCFTOOLS { ) ch_versions = ch_versions.mix(BCFTOOLS_CONCAT.out.versions.first()) + ch_vcf_tbi = Channel.empty() if(val_tabix) { TABIX_TABIX( BCFTOOLS_CONCAT.out.vcf diff --git a/subworkflows/local/vcf_filter_bcftools/main.nf b/subworkflows/local/vcf_filter_bcftools/main.nf index 6b3ef9d9..5b397d6c 100644 --- a/subworkflows/local/vcf_filter_bcftools/main.nf +++ b/subworkflows/local/vcf_filter_bcftools/main.nf @@ -25,6 +25,7 @@ workflow VCF_FILTER_BCFTOOLS { ) ch_versions = ch_versions.mix(FILTER_2.out.versions.first()) + ch_filter_vcfs = Channel.empty() if(val_tabix) { TABIX_TABIX( FILTER_2.out.vcf diff --git a/subworkflows/local/vcf_roh_automap/main.nf b/subworkflows/local/vcf_roh_automap/main.nf index 71fef123..24998f31 100644 --- a/subworkflows/local/vcf_roh_automap/main.nf +++ b/subworkflows/local/vcf_roh_automap/main.nf @@ -22,6 +22,7 @@ workflow VCF_ROH_AUTOMAP { } // Merge the repeat BED files from the container if no container has been given + ch_valid_repeats = Channel.empty() if (!ch_repeats) { AUTOMAP_REPEATS( Channel.value([[id:"${val_genome}_repeats"], val_genome]) diff --git a/subworkflows/local/vcf_upd_updio/main.nf b/subworkflows/local/vcf_upd_updio/main.nf index 19a37e37..7cfd7db4 100644 --- a/subworkflows/local/vcf_upd_updio/main.nf +++ b/subworkflows/local/vcf_upd_updio/main.nf @@ -16,11 +16,15 @@ workflow VCF_UPD_UPDIO { // Filter out all families that have less than 3 samples ch_vcfs - .filter { it[0].family_count >= 3 } + .filter { meta, vcf, tbi -> + meta.family_count >= 3 + } .set { ch_trio_vcfs } ch_peds - .filter { it[0].family_count >= 3 } + .filter { meta, ped -> + meta.family_count >= 3 + } .set { ch_trio_peds } CustomChannelOperators.joinOnKeys( @@ -33,7 +37,9 @@ workflow VCF_UPD_UPDIO { def meta_list = get_family_data_from_ped(meta, ped) [ meta_list, vcf, tbi ] } - .filter { it[0] } + .filter { meta, vcf, tbi -> + meta + } .transpose(by:0) .set { ch_trio_vcfs_family } From b96e08206fc4c420da877d6f386178482df761e8 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 28 Aug 2024 15:12:40 +0200 Subject: [PATCH 04/49] third batch of updates --- modules/local/automap/automap/main.nf | 22 +++++++++---------- modules/local/automap/repeats/main.nf | 3 --- modules/local/filter_beds/main.nf | 3 --- .../{merge_beds.nf => merge_beds/main.nf} | 3 --- modules/local/updio/main.nf | 3 --- 5 files changed, 10 insertions(+), 24 deletions(-) rename modules/local/{merge_beds.nf => merge_beds/main.nf} (96%) diff --git a/modules/local/automap/automap/main.nf b/modules/local/automap/automap/main.nf index f3090927..36072031 100644 --- a/modules/local/automap/automap/main.nf +++ b/modules/local/automap/automap/main.nf @@ -14,9 +14,6 @@ process AUTOMAP_AUTOMAP { tuple val(meta), path("${prefix}"), emit: automap path "versions.yml" , emit: versions - when: - task.ext.when == null || task.ext.when - script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" @@ -42,22 +39,23 @@ process AUTOMAP_AUTOMAP { stub: def args = task.ext.args ?: '' + def panel_name = args.contains("--panelname") ? args.split("--panelname")[-1].trim().split(" ")[0] : "" prefix = task.ext.prefix ?: "${meta.id}" - def create_outputs = meta.family_count > 1 ? (1..meta.family_count).collect { - def cmd_prefix = "touch ${prefix}/sample${it}" + def create_outputs = meta.family_count > 1 ? (1..meta.family_count).collect { number -> + def cmd_prefix = "touch ${prefix}/sample${number}" [ - "mkdir ${prefix}/sample${it}", - "${cmd_prefix}/sample${it}.HomRegions.pdf", - "${cmd_prefix}/sample${it}.HomRegions.${params.automap_panel_name}.tsv", - "${cmd_prefix}/sample${it}.HomRegions.tsv", - "${cmd_prefix}/sample${it}.HomRegions.strict.${params.automap_panel_name}.tsv" + "mkdir ${prefix}/sample${number}", + "${cmd_prefix}/sample${number}.HomRegions.pdf", + "${cmd_prefix}/sample${number}.HomRegions.${panel_name}.tsv", + "${cmd_prefix}/sample${number}.HomRegions.tsv", + "${cmd_prefix}/sample${number}.HomRegions.strict.${panel_name}.tsv" ].join(" && ") }.join(" && ") : [ "touch ${prefix}/${meta.id}.HomRegions.pdf", - "touch ${prefix}/${meta.id}.HomRegions.${params.automap_panel_name}.tsv", + "touch ${prefix}/${meta.id}.HomRegions.${panel_name}.tsv", "touch ${prefix}/${meta.id}.HomRegions.tsv", - "touch ${prefix}/${meta.id}.HomRegions.strict.${params.automap_panel_name}.tsv" + "touch ${prefix}/${meta.id}.HomRegions.strict.${panel_name}.tsv" ].join(" && ") def VERSION = "1.0.0" diff --git a/modules/local/automap/repeats/main.nf b/modules/local/automap/repeats/main.nf index 6bce529a..e5848023 100644 --- a/modules/local/automap/repeats/main.nf +++ b/modules/local/automap/repeats/main.nf @@ -11,9 +11,6 @@ process AUTOMAP_REPEATS { tuple val(meta), path("*.bed") , emit: repeats path "versions.yml" , emit: versions - when: - task.ext.when == null || task.ext.when - script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/local/filter_beds/main.nf b/modules/local/filter_beds/main.nf index 26e7dbd4..d7954da0 100644 --- a/modules/local/filter_beds/main.nf +++ b/modules/local/filter_beds/main.nf @@ -14,9 +14,6 @@ process FILTER_BEDS { tuple val(meta), path('*.bed'), emit: bed path "versions.yml" , emit: versions - when: - task.ext.when == null || task.ext.when - script: // Remove regions with no coverage from the callable regions BED file def args = task.ext.args ?: '' diff --git a/modules/local/merge_beds.nf b/modules/local/merge_beds/main.nf similarity index 96% rename from modules/local/merge_beds.nf rename to modules/local/merge_beds/main.nf index cc601495..5ead9159 100644 --- a/modules/local/merge_beds.nf +++ b/modules/local/merge_beds/main.nf @@ -15,9 +15,6 @@ process MERGE_BEDS { tuple val(meta), path('*.bed'), emit: bed path "versions.yml" , emit: versions - when: - task.ext.when == null || task.ext.when - script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/local/updio/main.nf b/modules/local/updio/main.nf index fa7b5f3a..2dfd7ef9 100644 --- a/modules/local/updio/main.nf +++ b/modules/local/updio/main.nf @@ -12,9 +12,6 @@ process UPDIO { tuple val(meta), path("${prefix}"), emit: updio path "versions.yml" , emit: versions - when: - task.ext.when == null || task.ext.when - script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" From a4581f2645b505ec799c4ed7da1513528809a5af Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 28 Aug 2024 16:27:10 +0200 Subject: [PATCH 05/49] fourth batch of updates --- modules.json | 2 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 14 +++- modules/nf-core/multiqc/meta.yml | 13 ++++ modules/nf-core/multiqc/tests/main.nf.test | 8 ++ .../nf-core/multiqc/tests/main.nf.test.snap | 20 ++--- modules/nf-core/multiqc/tests/nextflow.config | 5 ++ nextflow_schema.json | 16 ++-- .../local/input_split_bedtools/main.nf | 4 +- workflows/germline.nf | 74 ++++++++++++------- 10 files changed, 106 insertions(+), 52 deletions(-) create mode 100644 modules/nf-core/multiqc/tests/nextflow.config diff --git a/modules.json b/modules.json index e9fc85b7..1e2993d5 100644 --- a/modules.json +++ b/modules.json @@ -128,7 +128,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "19ca321db5d8bd48923262c2eca6422359633491", "installed_by": ["modules"] }, "rtgtools/format": { diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb67..a31464c9 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.24.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 47ac352f..ceaec139 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,14 +3,16 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.24.1--pyhdfd78af_0' : + 'biocontainers/multiqc:1.24.1--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) + path(replace_names) + path(sample_names) output: path "*multiqc_report.html", emit: report @@ -23,16 +25,22 @@ process MULTIQC { script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ $args \\ $config \\ + $prefix \\ $extra_config \\ $logo \\ + $replace \\ + $samples \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 45a9bc35..382c08cb 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -29,6 +29,19 @@ input: type: file description: Optional logo file for MultiQC pattern: "*.{png}" + - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: type: file diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f1c4242e..33316a7d 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -8,6 +8,8 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" + config "./nextflow.config" + test("sarscov2 single-end [fastqc]") { when { @@ -17,6 +19,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -41,6 +45,8 @@ nextflow_process { input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -66,6 +72,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index bfebd802..83fa080c 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:48:55.657331" + "timestamp": "2024-07-10T12:41:34.562023" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:49.071937" + "timestamp": "2024-07-10T11:27:11.933869532" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:25.457567" + "timestamp": "2024-07-10T11:26:56.709849369" } -} \ No newline at end of file +} diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config new file mode 100644 index 00000000..c537a6a3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = null + } +} diff --git a/nextflow_schema.json b/nextflow_schema.json index aa86f2d4..e1f4f3e2 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -4,7 +4,7 @@ "title": "nf-cmgg/germline pipeline parameters", "description": "A nextflow pipeline for calling and annotating variants", "type": "object", - "defs": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -682,25 +682,25 @@ }, "allOf": [ { - "$ref": "#/defs/input_output_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/defs/reference_genome_options" + "$ref": "#/$defs/reference_genome_options" }, { - "$ref": "#/defs/pipeline_specific_parameters" + "$ref": "#/$defs/pipeline_specific_parameters" }, { - "$ref": "#/defs/institutional_config_options" + "$ref": "#/$defs/institutional_config_options" }, { - "$ref": "#/defs/max_job_request_options" + "$ref": "#/$defs/max_job_request_options" }, { - "$ref": "#/defs/generic_options" + "$ref": "#/$defs/generic_options" }, { - "$ref": "#/defs/annotation_parameters" + "$ref": "#/$defs/annotation_parameters" } ] } diff --git a/subworkflows/local/input_split_bedtools/main.nf b/subworkflows/local/input_split_bedtools/main.nf index 54d76f54..b70140b5 100644 --- a/subworkflows/local/input_split_bedtools/main.nf +++ b/subworkflows/local/input_split_bedtools/main.nf @@ -35,6 +35,6 @@ workflow INPUT_SPLIT_BEDTOOLS { .set { ch_split_output } emit: - split = ch_split_output // channel: [ val(meta), path(input), path(input_index), path(bed) ] - versions = ch_versions // channel: [ versions.yml ] + split = ch_split_output // channel: [ val(meta), path(input), path(input_index), path(bed) ] + versions = ch_versions // channel: [ versions.yml ] } diff --git a/workflows/germline.nf b/workflows/germline.nf index 16f4aa25..7b51d93a 100644 --- a/workflows/germline.nf +++ b/workflows/germline.nf @@ -135,11 +135,11 @@ workflow GERMLINE { // Importing and convert the input files passed through the parameters to channels // - ch_fasta_ready = Channel.fromPath(fasta).map{ [[id:"reference"], it]}.collect() - ch_fai = fai ? Channel.fromPath(fai).map{ [[id:"reference"], it]}.collect() : null - ch_dict = dict ? Channel.fromPath(dict).map{ [[id:"reference"], it]}.collect() : null - ch_strtablefile = strtablefile ? Channel.fromPath(strtablefile).map{ [[id:"reference"], it]}.collect() : null - ch_sdf = sdf ? Channel.fromPath(sdf).map {sdf -> [[id:'reference'], sdf]}.collect() : null + ch_fasta_ready = Channel.fromPath(fasta).map{ fasta_file -> [[id:"reference"], fasta_file] }.collect() + ch_fai = fai ? Channel.fromPath(fai).map{ fai_file -> [[id:"reference"], fai_file] }.collect() : null + ch_dict = dict ? Channel.fromPath(dict).map{ dict_file -> [[id:"reference"], dict_file] }.collect() : null + ch_strtablefile = strtablefile ? Channel.fromPath(strtablefile).map{ str_file -> [[id:"reference"], str_file] }.collect() : null + ch_sdf = sdf ? Channel.fromPath(sdf).map { sdf_file -> [[id:'reference'], sdf_file] }.collect() : null ch_default_roi = roi ? Channel.fromPath(roi).collect() : [] @@ -152,12 +152,12 @@ workflow GERMLINE { ch_vcfanno_config = vcfanno_config ? Channel.fromPath(vcfanno_config).collect() : [] ch_vcfanno_lua = vcfanno_lua ? Channel.fromPath(vcfanno_lua).collect() : [] - ch_vcfanno_resources = vcfanno_resources ? Channel.of(vcfanno_resources.split(";")).map({ file(it, checkIfExists:true) }).collect() : [] + ch_vcfanno_resources = vcfanno_resources ? Channel.of(vcfanno_resources.split(";")).collect{ res -> file(res, checkIfExists:true) } : [] - ch_updio_common_cnvs = updio_common_cnvs ? Channel.fromPath(common_cnv_file).map { [[id:'updio_cnv'], it] } : [[],[]] + ch_updio_common_cnvs = updio_common_cnvs ? Channel.fromPath(updio_common_cnvs).map{ common_cnvs -> [[id:'updio_cnv'], common_cnvs] } : [[],[]] - ch_automap_repeats = automap_repeats ? Channel.fromPath(automap_repeats).map { [[id:"repeats"], it]}.collect() : [] - ch_automap_panel = automap_panel ? Channel.fromPath(automap_panel).map { [[id:"automap_panel"], it]}.collect() : [[],[]] + ch_automap_repeats = automap_repeats ? Channel.fromPath(automap_repeats).map{ repeats -> [[id:"repeats"], repeats] }.collect() : [] + ch_automap_panel = automap_panel ? Channel.fromPath(automap_panel).map{ panel -> [[id:"automap_panel"], panel] }.collect() : [[],[]] // // Check for the presence of EnsemblVEP plugins that use extra files @@ -221,7 +221,7 @@ workflow GERMLINE { // DBSNP index if (ch_dbsnp_ready && !ch_dbsnp_tbi) { TABIX_DBSNP( - ch_dbsnp_ready.map { [[id:'dbsnp'], it] } + ch_dbsnp_ready.map { dbnsp -> [[id:'dbsnp'], dbsnp] } ) ch_versions = ch_versions.mix(TABIX_DBSNP.out.versions) @@ -236,6 +236,7 @@ workflow GERMLINE { } // Reference fasta index + ch_fai_ready = Channel.empty() if (!ch_fai) { FAIDX( ch_fasta_ready, @@ -252,6 +253,7 @@ workflow GERMLINE { } // Reference sequence dictionary + ch_dict_ready = Channel.empty() if (!ch_dict) { CREATESEQUENCEDICTIONARY( ch_fasta_ready @@ -288,7 +290,7 @@ workflow GERMLINE { // Reference validation SDF if (validate && !ch_sdf) { RTGTOOLS_FORMAT( - ch_fasta_ready.map { meta, fasta -> [meta, fasta, [], []]} + ch_fasta_ready.map { meta, fasta_file -> [meta, fasta_file, [], []] } ) ch_versions = ch_versions.mix(RTGTOOLS_FORMAT.out.versions) @@ -318,7 +320,7 @@ workflow GERMLINE { ) ch_versions = ch_versions.mix(ENSEMBLVEP_DOWNLOAD.out.versions) - ch_vep_cache_ready = ENSEMBLVEP_DOWNLOAD.out.cache.map{it[1]}.collect() + ch_vep_cache_ready = ENSEMBLVEP_DOWNLOAD.out.cache.collect{ meta, cache -> cache } } else { ch_vep_cache_ready = ch_vep_cache } @@ -328,7 +330,7 @@ workflow GERMLINE { // ch_samplesheet - .multiMap { families, meta, cram, crai, gvcf, tbi, roi, truth_vcf, truth_tbi, truth_bed -> + .multiMap { families, meta, cram, crai, gvcf, tbi, roi_file, truth_vcf, truth_tbi, truth_bed -> // Divide the input files into their corresponding channel def new_meta = meta + [ family_count: families[meta.family].size(), // Contains the amount of samples in the family from this sample @@ -344,7 +346,7 @@ workflow GERMLINE { truth_variants: [new_meta_validation, truth_vcf, truth_tbi, truth_bed] // Optional channel containing the truth VCF, its index and the optional BED file gvcf: [new_meta, gvcf, tbi] // Optional channel containing the GVCFs and their optional indices cram: [new_meta, cram, crai] // Mandatory channel containing the CRAM files and their optional indices - roi: [new_meta, roi] // Optional channel containing the ROI BED files for WES samples + roi: [new_meta, roi_file] // Optional channel containing the ROI BED files for WES samples family_samples: [meta.family, families[meta.family]] // A channel containing the samples per family } .set { ch_input } @@ -356,7 +358,10 @@ workflow GERMLINE { // ch_input.gvcf - .filter { it[0].type == "gvcf" || it[0].type == "gvcf_cram" } // Filter out samples that have no GVCF + .filter { meta, gvcf, tbi -> + // Filter out samples that have no GVCF + meta.type == "gvcf" || meta.type == "gvcf_cram" + } .branch { meta, gvcf, tbi -> no_tbi: !tbi return [ meta, gvcf ] @@ -380,8 +385,14 @@ workflow GERMLINE { // CRAM_PREPARE_SAMTOOLS_BEDTOOLS( - ch_input.cram.filter { it[0].type == "cram" || (it[0].type == "gvcf_cram" && callers - GlobalVariables.gvcfCallers) }, // Filter out files that already have a called GVCF when only GVCF callers are used - ch_input.roi.filter { it[0].type == "cram" || (it[0].type == "gvcf_cram" && callers - GlobalVariables.gvcfCallers) }, // Filter out files that already have a called GVCF when only GVCF callers are used + ch_input.cram.filter { meta, cram, crai -> + // Filter out files that already have a called GVCF when only GVCF callers are used + meta.type == "cram" || (meta.type == "gvcf_cram" && callers - GlobalVariables.gvcfCallers) + }, + ch_input.roi.filter { meta, roi_file -> + // Filter out files that already have a called GVCF when only GVCF callers are used + meta.type == "cram" || (meta.type == "gvcf_cram" && callers - GlobalVariables.gvcfCallers) + }, ch_fasta_ready, ch_fai_ready, ch_default_roi @@ -393,7 +404,9 @@ workflow GERMLINE { // INPUT_SPLIT_BEDTOOLS( - CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.ready_beds.map { it + [scatter_count] }, + CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.ready_beds.map { meta, bed -> + [meta, bed, scatter_count] + }, CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.ready_crams ) ch_versions = ch_versions.mix(INPUT_SPLIT_BEDTOOLS.out.versions) @@ -406,7 +419,10 @@ workflow GERMLINE { // CRAM_CALL_GENOTYPE_GATK4( - INPUT_SPLIT_BEDTOOLS.out.split.filter { it[0].type == "cram" }, // Filter out the entries that already have a GVCF + INPUT_SPLIT_BEDTOOLS.out.split.filter { meta, cram, crai, bed -> + // Filter out the entries that already have a GVCF + meta.type == "cram" + }, ch_gvcfs_ready, ch_fasta_ready, ch_fai_ready, @@ -462,8 +478,9 @@ workflow GERMLINE { [[],[]] ) ch_versions = ch_versions.mix(BCFTOOLS_STATS.out.versions.first()) - ch_reports = ch_reports.mix(BCFTOOLS_STATS.out.stats.collect { it[1] }) + ch_reports = ch_reports.mix(BCFTOOLS_STATS.out.stats.collect { meta, report -> report }) + ch_normalized_variants = Channel.empty() if(normalize) { BCFTOOLS_NORM( ch_called_variants, @@ -489,7 +506,6 @@ workflow GERMLINE { // Preprocess the PED channel // - ch_normalized_variants .map { meta, vcf, tbi -> [ meta, pedFiles.containsKey(meta.family) ? pedFiles[meta.family] : [] ] @@ -502,8 +518,8 @@ workflow GERMLINE { VCF_EXTRACT_RELATE_SOMALIER( ch_normalized_variants, - ch_fasta_ready.map { it[1] }, - ch_fai_ready.map { it[1] }, + ch_fasta_ready.map { meta, fasta_file -> fasta_file }, + ch_fai_ready.map { meta, fai_file -> fai_file }, ch_somalier_sites, ch_somalier_input ) @@ -513,6 +529,7 @@ workflow GERMLINE { // Add PED headers to the VCFs // + ch_ped_vcfs = Channel.empty() if(add_ped){ VCF_PED_RTGTOOLS( @@ -535,6 +552,7 @@ workflow GERMLINE { // Annotation of the variants and creation of Gemini-compatible database files // + ch_annotation_output = Channel.empty() if (annotate) { VCF_ANNOTATION( ch_ped_vcfs, @@ -584,9 +602,9 @@ workflow GERMLINE { .groupTuple() // No size needed here since it's being run before any process .map { meta, vcf, tbi, bed -> // Get only one VCF for samples that were given multiple times - one_vcf = vcf.find { it != [] } ?: [] - one_tbi = tbi.find { it != [] } ?: [] - one_bed = bed.find { it != [] } ?: [] + one_vcf = vcf.find { vcf_file -> vcf_file != [] } ?: [] + one_tbi = tbi.find { tbi_file -> tbi_file != [] } ?: [] + one_bed = bed.find { bed_file -> bed_file != [] } ?: [] [ meta, one_vcf, one_tbi, one_bed ] } .branch { meta, vcf, tbi, bed -> @@ -757,7 +775,9 @@ workflow GERMLINE { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() + ch_multiqc_logo.toList(), + [], + [] ) emit: From fcb0d192ed51721d8fc3da9337157ff6183e33f5 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 29 Aug 2024 09:47:12 +0200 Subject: [PATCH 06/49] update configs --- conf/base.config | 34 +++++++++--------- conf/empty.config | 1 + conf/empty_genomes.config | 3 ++ conf/modules.config | 10 +++--- conf/nf_test.config | 14 +++++--- conf/test.config | 14 +++++--- docs/parameters.md | 10 ------ nextflow.config | 76 +++++---------------------------------- nextflow_schema.json | 38 -------------------- tests/nextflow.config | 14 ++++---- 10 files changed, 59 insertions(+), 155 deletions(-) create mode 100644 conf/empty.config create mode 100644 conf/empty_genomes.config diff --git a/conf/base.config b/conf/base.config index 732c5444..35b35265 100644 --- a/conf/base.config +++ b/conf/base.config @@ -10,9 +10,9 @@ process { - cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 * task.attempt } + memory = { 8.GB * task.attempt } + time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 @@ -20,30 +20,30 @@ process { // Process-specific resource requirements withLabel:process_single { - cpus = { check_max( 1 , 'cpus' ) } - memory = { check_max( 8.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 } + memory = { 8.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 16.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 2 * task.attempt } + memory = { 16.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_medium { - cpus = { check_max( 4 * task.attempt, 'cpus' ) } - memory = { check_max( 32.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + cpus = { 4 * task.attempt } + memory = { 32.GB * task.attempt } + time = { 8.h * task.attempt } } withLabel:process_high { - cpus = { check_max( 8 * task.attempt, 'cpus' ) } - memory = { check_max( 64.GB * task.attempt, 'memory' ) } - time = { check_max( 16.h * task.attempt, 'time' ) } + cpus = { 8 * task.attempt } + memory = { 64.GB * task.attempt } + time = { 16.h * task.attempt } } withLabel:process_long { - time = { check_max( 20.h * task.attempt, 'time' ) } + time = { 20.h * task.attempt } } withLabel:process_high_memory { - memory = { check_max( 200.GB * task.attempt, 'memory' ) } + memory = { 200.GB * task.attempt } } withLabel:error_ignore { errorStrategy = 'ignore' diff --git a/conf/empty.config b/conf/empty.config new file mode 100644 index 00000000..11f237e6 --- /dev/null +++ b/conf/empty.config @@ -0,0 +1 @@ +// DON'T REMOVE THIS FILE \ No newline at end of file diff --git a/conf/empty_genomes.config b/conf/empty_genomes.config new file mode 100644 index 00000000..e02e8342 --- /dev/null +++ b/conf/empty_genomes.config @@ -0,0 +1,3 @@ +// DON'T REMOVE THIS FILE! + +params.genomes = [:] \ No newline at end of file diff --git a/conf/modules.config b/conf/modules.config index 14da9639..f8f93e8f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -138,7 +138,7 @@ process { } withName: "^.*CRAM_CALL_GENOTYPE_GATK4:CRAM_CALL_GATK4:GATK4_HAPLOTYPECALLER\$" { - time = { check_max( 16.h * task.attempt, 'time' ) } + time = { 16.h * task.attempt } ext.prefix = {"${meta.id}.g"} ext.args = { [ @@ -209,7 +209,7 @@ process { withName: "^.*CRAM_CALL_GENOTYPE_GATK4:GVCF_JOINT_GENOTYPE_GATK4:GATK4_GENOMICSDBIMPORT\$" { label = { meta.family_count <= 10 ? "process_medium" : "process_high" } - time = { check_max( 16.h * task.attempt, 'time' ) } + time = { 16.h * task.attempt } // Lots of parameters are fetched from https://gatk.broadinstitute.org/hc/en-us/articles/360056138571-GenomicsDBImport-usage-and-performance-guidelines ext.args = { [ @@ -236,7 +236,7 @@ process { if(!params.only_merge) { withName: "^.*CRAM_CALL_GENOTYPE_GATK4:GVCF_JOINT_GENOTYPE_GATK4:GATK4_GENOTYPEGVCFS\$" { - time = { check_max( 16.h * task.attempt, 'time' ) } + time = { 16.h * task.attempt } ext.args = { [ "--allow-old-rms-mapping-quality-annotation-data", @@ -288,7 +288,7 @@ process { if("vardict" in callers) { withName: "^.*CRAM_CALL_VARDICTJAVA:VARDICTJAVA\$" { - time = { check_max( 16.h * task.attempt, 'time' ) } + time = { 16.h * task.attempt } ext.prefix = {"${meta.id}"} ext.args = { [ @@ -430,7 +430,7 @@ process { if(params.annotate){ withName: "^.*VCF_ANNOTATION:VCF_ANNOTATE_ENSEMBLVEP:ENSEMBLVEP_VEP\$" { - memory = { check_max( 12.GB * task.attempt, 'memory' ) } + memory = { 12.GB * task.attempt } ext.args = {[ // Specify the input format "--format vcf", diff --git a/conf/nf_test.config b/conf/nf_test.config index 8442cb9d..a592580c 100644 --- a/conf/nf_test.config +++ b/conf/nf_test.config @@ -6,11 +6,6 @@ params { - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data input = "${baseDir}/tests/inputs/samplesheet.csv" @@ -25,3 +20,12 @@ params { skip_date_project = true } + +process { + // Limit resources so that this can run on GitHub Actions + resourceLimits = [ + cpus : 2, + memory: 6.GB, + time : 6.h + ] +} \ No newline at end of file diff --git a/conf/test.config b/conf/test.config index 0d2a33a3..01e51012 100644 --- a/conf/test.config +++ b/conf/test.config @@ -14,11 +14,6 @@ params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data input = "${projectDir}/assets/samplesheet.csv" @@ -55,3 +50,12 @@ params { vcfanno_resources = "https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz;https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz.tbi" } + +process { + // Limit resources so that this can run on GitHub Actions + resourceLimits = [ + cpus : 2, + memory: 6.GB, + time : 6.h + ] +} diff --git a/docs/parameters.md b/docs/parameters.md index 65da21a8..d4f25095 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -81,16 +81,6 @@ Parameters used to describe centralised config profiles. These should not be edi | `config_profile_contact` | Institutional config contact information. | `string` | | | True | | `config_profile_url` | Institutional config URL link. | `string` | | | True | -## Max job request options - -Set the top limit for requested resources for any single job. - -| Parameter | Description | Type | Default | Required | Hidden | -| ------------ | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------- | ------- | -------- | ------ | -| `max_cpus` | Maximum number of CPUs that can be requested for any single job.
    HelpUse to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`
    | `integer` | 16 | | True | -| `max_memory` | Maximum amount of memory that can be requested for any single job.
    HelpUse to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`
    | `string` | 128.GB | | True | -| `max_time` | Maximum amount of time that can be requested for any single job.
    HelpUse to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`
    | `string` | 240.h | | True | - ## Generic options Less common options for the pipeline, typically set in a config file. diff --git a/nextflow.config b/nextflow.config index 807afbb9..507de067 100644 --- a/nextflow.config +++ b/nextflow.config @@ -104,12 +104,6 @@ params { config_profile_contact = null config_profile_url = null - // Max resource options - // Defaults only, expecting to be overwritten - max_memory = '128.GB' - max_cpus = 16 - max_time = '240.h' - // Schema validation default options validate_params = true @@ -119,22 +113,10 @@ params { includeConfig 'conf/base.config' // Load nf-core custom profiles from different Institutions -try { - includeConfig "${params.custom_config_base}/nfcore_custom.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -} - -// Load nf-cmgg/germline custom profiles from different institutions. -// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs! -// try { -// includeConfig "${params.custom_config_base}/pipeline/germline.config" -// } catch (Exception e) { -// System.err.println("WARNING: Could not load nf-core/config/germline profiles: ${params.custom_config_base}/pipeline/germline.config") -// } +includeConfig { !System.getenv('NXF_OFFLINE') ? "${params.custom_config_base}/nfcore_custom.config" : "conf/empty.config" } // Include test data config -includeConfig 'https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/nf-cmgg-testdata.config' +includeConfig { !System.getenv('NXF_OFFLINE') ? 'https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/nf-cmgg-testdata.config' : "conf/empty.config" } profiles { debug { @@ -255,7 +237,7 @@ singularity.registry = 'quay.io' // Nextflow plugins plugins { - id 'nf-schema@2.0.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.1.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { @@ -271,14 +253,8 @@ validation { } } -// Load igenomes.config if required -if (!params.igenomes_ignore) { - includeConfig "conf/igenomes.config" -} else if (!params.genomes_ignore){ - includeConfig "https://raw.githubusercontent.com/nf-cmgg/configs/main/conf/Hsapiens/genomes.config" -} else { - params.genomes = [:] -} +includeConfig { !params.igenomes_ignore ? "conf/igenomes.config" : !params.genomes_ignore ? "https://raw.githubusercontent.com/nf-cmgg/configs/main/conf/Hsapiens/genomes.config" : "conf/empty_genomes.config" } + // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -296,22 +272,21 @@ process.shell = ['/bin/bash', '-euo', 'pipefail'] // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false -def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_timeline_${new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')}.html" } report { enabled = true - file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" + file = timeline.file.replace("timeline", "report") } trace { enabled = true - file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" + file = timeline.file.replace("timeline", "trace") } dag { enabled = true - file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" + file = timeline.file.replace("execution_timeline", "pipeline_dag") } manifest { @@ -327,36 +302,3 @@ manifest { // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' - -// Function to ensure that resource requirements don't go beyond -// a maximum limit -def check_max(obj, type) { - if (type == 'memory') { - try { - if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) - return params.max_memory as nextflow.util.MemoryUnit - else - return obj - } catch (all) { - println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'time') { - try { - if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) - return params.max_time as nextflow.util.Duration - else - return obj - } catch (all) { - println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'cpus') { - try { - return Math.min( obj, params.max_cpus as int ) - } catch (all) { - println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" - return obj - } - } -} diff --git a/nextflow_schema.json b/nextflow_schema.json index e1f4f3e2..811aa9bf 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -354,41 +354,6 @@ } } }, - "max_job_request_options": { - "title": "Max job request options", - "type": "object", - "fa_icon": "fab fa-acquisitions-incorporated", - "description": "Set the top limit for requested resources for any single job.", - "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", - "properties": { - "max_cpus": { - "type": "integer", - "description": "Maximum number of CPUs that can be requested for any single job.", - "default": 16, - "fa_icon": "fas fa-microchip", - "hidden": true, - "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" - }, - "max_memory": { - "type": "string", - "description": "Maximum amount of memory that can be requested for any single job.", - "default": "128.GB", - "fa_icon": "fas fa-memory", - "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", - "hidden": true, - "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" - }, - "max_time": { - "type": "string", - "description": "Maximum amount of time that can be requested for any single job.", - "default": "240.h", - "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", - "hidden": true, - "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" - } - } - }, "generic_options": { "title": "Generic options", "type": "object", @@ -693,9 +658,6 @@ { "$ref": "#/$defs/institutional_config_options" }, - { - "$ref": "#/$defs/max_job_request_options" - }, { "$ref": "#/$defs/generic_options" }, diff --git a/tests/nextflow.config b/tests/nextflow.config index 9a3681e3..59ffd5da 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -7,11 +7,6 @@ // Change some params to test data params { - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - input = "${baseDir}/tests/inputs/samplesheet.csv" // References for test data @@ -67,7 +62,10 @@ params { } process { - cpus = 2 - memory = 3.GB - time = 2.h + // Limit resources so that this can run on GitHub Actions + resourceLimits = [ + cpus : 2, + memory: 6.GB, + time : 6.h + ] } From 70e8c24546f05edf60b8a8312a7f56dfa5f5c965 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 29 Aug 2024 09:49:28 +0200 Subject: [PATCH 07/49] update changelog --- CHANGELOG.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index f8553db3..315d1fe8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,13 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v1.8.0dev + +## Refactors + +1. Updated the pipeline to the new linting guidelines +2. Removed `check_max` in favor of `resourceLimits` + ## v1.7.0 - Tolerant Tongeren - [August 9 2024] ## Fixes From d46f82d8412c9253a57665683e268f3bb0e00f57 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 29 Aug 2024 11:09:30 +0200 Subject: [PATCH 08/49] update config includes --- nextflow.config | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/nextflow.config b/nextflow.config index 507de067..6fad50d6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -113,10 +113,10 @@ params { includeConfig 'conf/base.config' // Load nf-core custom profiles from different Institutions -includeConfig { !System.getenv('NXF_OFFLINE') ? "${params.custom_config_base}/nfcore_custom.config" : "conf/empty.config" } +includeConfig !System.getenv('NXF_OFFLINE') ? "${params.custom_config_base}/nfcore_custom.config" : "conf/empty.config" // Include test data config -includeConfig { !System.getenv('NXF_OFFLINE') ? 'https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/nf-cmgg-testdata.config' : "conf/empty.config" } +includeConfig !System.getenv('NXF_OFFLINE') ? 'https://raw.githubusercontent.com/nf-cmgg/test-datasets/main/nf-cmgg-testdata.config' : "conf/empty.config" profiles { debug { @@ -132,7 +132,6 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false - conda.channels = ['conda-forge', 'bioconda', 'defaults'] apptainer.enabled = false } mamba { @@ -253,7 +252,7 @@ validation { } } -includeConfig { !params.igenomes_ignore ? "conf/igenomes.config" : !params.genomes_ignore ? "https://raw.githubusercontent.com/nf-cmgg/configs/main/conf/Hsapiens/genomes.config" : "conf/empty_genomes.config" } +includeConfig !params.igenomes_ignore ? "conf/igenomes.config" : !params.genomes_ignore ? "https://raw.githubusercontent.com/nf-cmgg/configs/main/conf/Hsapiens/genomes.config" : "conf/empty_genomes.config" // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. From a35e9c283218188138a25ab0ae16d07f10814871 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 29 Aug 2024 11:13:08 +0200 Subject: [PATCH 09/49] use nf-core dev for linting --- .github/workflows/linting.yml | 2 +- nextflow_schema.json | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 1fcafe88..49fb4340 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -44,7 +44,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core + pip install git+https://github.com/nf-core/tools@dev - name: Run nf-core lint env: diff --git a/nextflow_schema.json b/nextflow_schema.json index 811aa9bf..34ed7abd 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -132,8 +132,7 @@ "genomes": { "type": "object", "description": "A map structure containing the paths to all genome references", - "hidden": true, - "default": {} + "hidden": true } }, "required": ["fasta"] From a06b09a59442287691cad4bf88c295ee506897c3 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 29 Aug 2024 11:19:10 +0200 Subject: [PATCH 10/49] bump minimal nextflow version --- .github/workflows/ci.yml | 2 +- CHANGELOG.md | 4 ++++ nextflow.config | 2 +- 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 8bbcff4d..37ebe5ce 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -24,7 +24,7 @@ jobs: strategy: matrix: NXF_VER: - - "23.10.0" + - "24.04.0" - "latest-everything" test: - "pipeline_default" diff --git a/CHANGELOG.md b/CHANGELOG.md index 315d1fe8..0e59e9f4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v1.8.0dev +## Changes + +1. Bumped the minimal support nextflow version to `24.04.0` + ## Refactors 1. Updated the pipeline to the new linting guidelines diff --git a/nextflow.config b/nextflow.config index 6fad50d6..12e7effa 100644 --- a/nextflow.config +++ b/nextflow.config @@ -294,7 +294,7 @@ manifest { homePage = 'https://github.com/nf-cmgg/germline' description = """A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data""" mainScript = 'main.nf' - nextflowVersion = '!>=23.10.0' + nextflowVersion = '!>=24.04.0' version = '1.8.0dev' doi = '' } From ee0b5373e6913b27079e79bbee3d839c4a541f30 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 29 Aug 2024 12:43:01 +0200 Subject: [PATCH 11/49] remove whitespace --- subworkflows/local/cram_prepare_samtools_bedtools/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/cram_prepare_samtools_bedtools/main.nf b/subworkflows/local/cram_prepare_samtools_bedtools/main.nf index b18f003b..b4cdbef5 100644 --- a/subworkflows/local/cram_prepare_samtools_bedtools/main.nf +++ b/subworkflows/local/cram_prepare_samtools_bedtools/main.nf @@ -95,7 +95,7 @@ workflow CRAM_PREPARE_SAMTOOLS_BEDTOOLS { if(entry != []){ output_roi.add(entry) is_present = true - } + } } found: is_present return [ meta, output_roi ] From 42ff0b143c551f906b7b74663b380e4330f4ced3 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 3 Sep 2024 17:19:35 +0200 Subject: [PATCH 12/49] first steps --- .nf-core.yml | 6 +- CITATIONS.md | 1 + modules.json | 78 +-- .../bcftools/concat/bcftools-concat.diff | 40 -- .../nf-core/bcftools/concat/environment.yml | 2 +- modules/nf-core/bcftools/concat/main.nf | 31 +- modules/nf-core/bcftools/concat/meta.yml | 8 + .../bcftools/concat/tests/main.nf.test | 254 ++++++- .../bcftools/concat/tests/main.nf.test.snap | 370 ++++++++++- .../bcftools/concat/tests/vcf_gz_index.config | 4 + .../concat/tests/vcf_gz_index_csi.config | 4 + .../concat/tests/vcf_gz_index_tbi.config | 4 + .../bcftools/pluginscatter/environment.yml | 2 +- .../nf-core/bcftools/pluginscatter/main.nf | 24 +- .../nf-core/bcftools/pluginscatter/meta.yml | 8 + .../bcftools/pluginscatter/tests/main.nf.test | 415 ++++++++++++ .../pluginscatter/tests/main.nf.test.snap | 623 ++++++++++++++++++ .../pluginscatter/tests/nextflow.config | 3 + .../bcftools/pluginscatter/tests/tags.yml | 2 + .../pluginscatter/tests/vcf_gz_index.config | 4 + .../tests/vcf_gz_index_csi.config | 4 + .../tests/vcf_gz_index_tbi.config | 4 + modules/nf-core/bcftools/sort/environment.yml | 2 +- modules/nf-core/bcftools/sort/main.nf | 19 +- modules/nf-core/bcftools/sort/meta.yml | 8 + .../nf-core/bcftools/sort/tests/main.nf.test | 222 +++++++ .../bcftools/sort/tests/main.nf.test.snap | 350 ++++++++++ modules/nf-core/bcftools/sort/tests/tags.yml | 2 + .../bcftools/sort/tests/vcf_gz_index.config | 4 + .../sort/tests/vcf_gz_index_csi.config | 4 + .../sort/tests/vcf_gz_index_tbi.config | 4 + .../ensemblvep/vep/ensemblvep-vep.diff | 38 -- .../nf-core/ensemblvep/vep/environment.yml | 4 +- modules/nf-core/ensemblvep/vep/main.nf | 18 +- modules/nf-core/ensemblvep/vep/meta.yml | 6 +- .../nf-core/ensemblvep/vep/tests/main.nf.test | 114 ++++ .../ensemblvep/vep/tests/main.nf.test.snap | 26 + .../ensemblvep/vep/tests/nextflow.config | 12 + .../ensemblvep/vep/tests/tab.gz.config | 5 + modules/nf-core/ensemblvep/vep/tests/tags.yml | 2 + .../nf-core/ensemblvep/vep/tests/vcf.config | 5 + modules/nf-core/happy/happy/environment.yml | 7 - modules/nf-core/happy/happy/main.nf | 84 --- modules/nf-core/happy/happy/meta.yml | 114 ---- modules/nf-core/snpeff/snpeff/main.nf | 10 +- .../nf-core/snpeff/snpeff/tests/main.nf.test | 51 ++ .../snpeff/snpeff/tests/main.nf.test.snap | 31 + .../snpeff/snpeff/tests/nextflow.config | 4 + modules/nf-core/snpeff/snpeff/tests/tags.yml | 2 + modules/nf-core/tabix/tabix/environment.yml | 3 + modules/nf-core/tabix/tabix/main.nf | 13 +- .../nf-core/tabix/tabix/tests/main.nf.test | 136 ++++ .../tabix/tabix/tests/main.nf.test.snap | 212 ++++++ .../tabix/tabix/tests/tabix_bed.config | 5 + .../tabix/tabix/tests/tabix_gff.config | 5 + .../tabix/tabix/tests/tabix_vcf_csi.config | 5 + .../tabix/tabix/tests/tabix_vcf_tbi.config | 5 + modules/nf-core/tabix/tabix/tests/tags.yml | 2 + modules/nf-core/vcf2db/vcf2db.diff | 143 ---- 59 files changed, 3010 insertions(+), 558 deletions(-) create mode 120000 CITATIONS.md delete mode 100644 modules/nf-core/bcftools/concat/bcftools-concat.diff create mode 100644 modules/nf-core/bcftools/concat/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config create mode 100644 modules/nf-core/bcftools/pluginscatter/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/pluginscatter/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/pluginscatter/tests/nextflow.config create mode 100644 modules/nf-core/bcftools/pluginscatter/tests/tags.yml create mode 100644 modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_tbi.config create mode 100644 modules/nf-core/bcftools/sort/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/sort/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/sort/tests/tags.yml create mode 100644 modules/nf-core/bcftools/sort/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/sort/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/sort/tests/vcf_gz_index_tbi.config delete mode 100644 modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff create mode 100644 modules/nf-core/ensemblvep/vep/tests/main.nf.test create mode 100644 modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap create mode 100644 modules/nf-core/ensemblvep/vep/tests/nextflow.config create mode 100644 modules/nf-core/ensemblvep/vep/tests/tab.gz.config create mode 100644 modules/nf-core/ensemblvep/vep/tests/tags.yml create mode 100644 modules/nf-core/ensemblvep/vep/tests/vcf.config delete mode 100644 modules/nf-core/happy/happy/environment.yml delete mode 100644 modules/nf-core/happy/happy/main.nf delete mode 100644 modules/nf-core/happy/happy/meta.yml create mode 100644 modules/nf-core/snpeff/snpeff/tests/main.nf.test create mode 100644 modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap create mode 100644 modules/nf-core/snpeff/snpeff/tests/nextflow.config create mode 100644 modules/nf-core/snpeff/snpeff/tests/tags.yml create mode 100644 modules/nf-core/tabix/tabix/tests/main.nf.test create mode 100644 modules/nf-core/tabix/tabix/tests/main.nf.test.snap create mode 100644 modules/nf-core/tabix/tabix/tests/tabix_bed.config create mode 100644 modules/nf-core/tabix/tabix/tests/tabix_gff.config create mode 100644 modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config create mode 100644 modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config create mode 100644 modules/nf-core/tabix/tabix/tests/tags.yml delete mode 100644 modules/nf-core/vcf2db/vcf2db.diff diff --git a/.nf-core.yml b/.nf-core.yml index f9c0a042..70105d4f 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -7,17 +7,15 @@ lint: - .github/ISSUE_TEMPLATE/config.yml - .github/workflows/awstest.yml - .github/workflows/awsfulltest.yml + - docs/README.md files_unchanged: - CODE_OF_CONDUCT.md - assets/nf-core-germline_logo_light.png - docs/images/nf-core-germline_logo_light.png - docs/images/nf-core-germline_logo_dark.png - .github/ISSUE_TEMPLATE/bug_report.yml - multiqc_config: - - report_comment nextflow_config: - - manifest.name - - manifest.homePage + - "custom_config" nf_core_version: 2.14.1 repository_type: pipeline template: diff --git a/CITATIONS.md b/CITATIONS.md new file mode 120000 index 00000000..35cfd9f8 --- /dev/null +++ b/CITATIONS.md @@ -0,0 +1 @@ +docs/CITATIONS.md \ No newline at end of file diff --git a/modules.json b/modules.json index 1e2993d5..830e32fa 100644 --- a/modules.json +++ b/modules.json @@ -12,9 +12,8 @@ }, "bcftools/concat": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff"], - "patch": "modules/nf-core/bcftools/concat/bcftools-concat.diff" + "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/filter": { "branch": "master", @@ -28,7 +27,7 @@ }, "bcftools/pluginscatter": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", + "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/query": { @@ -39,17 +38,16 @@ "bcftools/reheader": { "branch": "master", "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": ["modules"], - "patch": "modules/nf-core/bcftools/reheader/bcftools-reheader.diff" + "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", + "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/stats": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", + "git_sha": "618364f55cb88f6c283f6c6c45c24d5f9f08f998", "installed_by": ["modules"] }, "bedtools/intersect": { @@ -59,66 +57,57 @@ }, "bedtools/merge": { "branch": "master", - "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", + "git_sha": "a3d614e4a7b8691a259bcfe33ad80903217d6215", "installed_by": ["modules"] }, "bedtools/split": { "branch": "master", - "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", + "git_sha": "6dc8a32e32158bb4d3f9af92c802233b5d4f8e4d", "installed_by": ["modules"] }, "ensemblvep/download": { "branch": "master", - "git_sha": "214d575774c172062924ad3564b4f66655600730", - "installed_by": ["modules"], - "patch": "modules/nf-core/ensemblvep/download/ensemblvep-download.diff" + "git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0", + "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", - "git_sha": "1b5ffd7aa6e3c21b702957c808cbd1c351dd1809", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"], - "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" + "git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0", + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "gatk4/calibratedragstrmodel": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", + "git_sha": "3f42e07a1133064c569b0dbe182979527bca9e59", "installed_by": ["modules"] }, "gatk4/composestrtablefile": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", + "git_sha": "926e2f394d01c71d3abbdbca9c588630bfe51abf", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", + "git_sha": "e6fe277739f5894711405af3e717b2470bd956b5", "installed_by": ["modules"] }, "gatk4/genomicsdbimport": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", "installed_by": ["modules"] }, "gatk4/genotypegvcfs": { "branch": "master", "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", - "installed_by": ["modules"], - "patch": "modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff" + "installed_by": ["modules"] }, "gatk4/haplotypecaller": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", - "installed_by": ["modules"], - "patch": "modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff" - }, - "gawk": { - "branch": "master", - "git_sha": "dc3527855e7358c6d8400828754c0caa5f11698f", + "git_sha": "e53d091a6de1ae9fd681351c085d8abe076ba1ec", "installed_by": ["modules"] }, - "happy/happy": { + "gawk": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "da4d05d04e65227d4307e87940842f1a14de62c7", "installed_by": ["modules"] }, "mosdepth": { @@ -138,9 +127,8 @@ }, "rtgtools/pedfilter": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"], - "patch": "modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff" + "git_sha": "1a4ab76618a2269ee653aefff8a5ee1f855e5f83", + "installed_by": ["modules"] }, "rtgtools/rocplot": { "branch": "master", @@ -170,12 +158,11 @@ "samtools/merge": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["modules"], - "patch": "modules/nf-core/samtools/merge/samtools-merge.diff" + "installed_by": ["modules"] }, "snpeff/snpeff": { "branch": "master", - "git_sha": "214d575774c172062924ad3564b4f66655600730", + "git_sha": "3ad7292d9b8da881386e9d5b58364d7da489b38b", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "somalier/extract": { @@ -185,9 +172,8 @@ }, "somalier/relate": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"], - "patch": "modules/nf-core/somalier/relate/somalier-relate.diff" + "git_sha": "d8ba32c6b54a01f8efa7b51a1f3978f003f8873b", + "installed_by": ["modules"] }, "tabix/bgzip": { "branch": "master", @@ -201,7 +187,7 @@ }, "tabix/tabix": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff"] }, "untar": { @@ -212,18 +198,16 @@ "vardictjava": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"], - "patch": "modules/nf-core/vardictjava/vardictjava.diff" + "installed_by": ["modules"] }, "vcf2db": { "branch": "master", - "git_sha": "527a80a28d9a54e5fd3626168ab72b063c11fbb2", - "installed_by": ["modules"], - "patch": "modules/nf-core/vcf2db/vcf2db.diff" + "git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d", + "installed_by": ["modules"] }, "vcfanno": { "branch": "master", - "git_sha": "b558cd24f8751dcda51f957391f5f9cb83e28586", + "git_sha": "9a8bba5910982ae637dedb8664e3121db77e173f", "installed_by": ["modules"] } } diff --git a/modules/nf-core/bcftools/concat/bcftools-concat.diff b/modules/nf-core/bcftools/concat/bcftools-concat.diff deleted file mode 100644 index 980df77a..00000000 --- a/modules/nf-core/bcftools/concat/bcftools-concat.diff +++ /dev/null @@ -1,40 +0,0 @@ -Changes in module 'nf-core/bcftools/concat' ---- modules/nf-core/bcftools/concat/main.nf -+++ modules/nf-core/bcftools/concat/main.nf -@@ -8,7 +8,7 @@ - 'biocontainers/bcftools:1.18--h8b25389_0' }" - - input: -- tuple val(meta), path(vcfs), path(tbi) -+ tuple val(meta), path(vcfs), path(tbis) - - output: - tuple val(meta), path("*.gz"), emit: vcf -@@ -19,8 +19,11 @@ - - script: - def args = task.ext.args ?: '' -- prefix = task.ext.prefix ?: "${meta.id}" -+ def prefix = task.ext.prefix ?: "${meta.id}" -+ def create_tbis = vcfs.collect { it.extension == 'gz' && !tbis ? " tabix ${it}" : "" } -+ - """ -+ ${create_tbis.join("\n")} - bcftools concat \\ - --output ${prefix}.vcf.gz \\ - $args \\ -@@ -34,8 +37,11 @@ - """ - - stub: -- prefix = task.ext.prefix ?: "${meta.id}" -+ def prefix = task.ext.prefix ?: "${meta.id}" -+ def create_tbis = vcfs.collect { it.extension == 'gz' && !tbis ? " touch ${it}.tbi" : "" } -+ - """ -+ ${create_tbis.join("\n")} - touch ${prefix}.vcf.gz - - cat <<-END_VERSIONS > versions.yml - -************************************************************ diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml index ff0200df..6544e949 100644 --- a/modules/nf-core/bcftools/concat/environment.yml +++ b/modules/nf-core/bcftools/concat/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index eaefbe73..e2337eff 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -4,26 +4,25 @@ process BCFTOOLS_CONCAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: - tuple val(meta), path(vcfs), path(tbis) + tuple val(meta), path(vcfs), path(tbi) output: - tuple val(meta), path("*.gz"), emit: vcf - path "versions.yml" , emit: versions + tuple val(meta), path("*.gz") , emit: vcf + tuple val(meta), path("*.tbi"), emit: tbi, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def create_tbis = vcfs.collect { it.extension == 'gz' && !tbis ? " tabix ${it}" : "" } - + def prefix = task.ext.prefix ?: "${meta.id}" """ - ${create_tbis.join("\n")} bcftools concat \\ --output ${prefix}.vcf.gz \\ $args \\ @@ -37,12 +36,16 @@ process BCFTOOLS_CONCAT { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" - def create_tbis = vcfs.collect { it.extension == 'gz' && !tbis ? " touch ${it}.tbi" : "" } - + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_index = index.matches("csi|tbi") ? "touch ${prefix}.vcf.gz.${index}" : "" """ - ${create_tbis.join("\n")} - touch ${prefix}.vcf.gz + echo "" | gzip > ${prefix}.vcf.gz + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml index 91cb54d5..eeeb2071 100644 --- a/modules/nf-core/bcftools/concat/meta.yml +++ b/modules/nf-core/bcftools/concat/meta.yml @@ -39,6 +39,14 @@ output: type: file description: VCF concatenated output file pattern: "*.{vcf.gz}" + - csi: + type: file + description: Default VCF file index + pattern: "*.csi" + - tbi: + type: file + description: Alternative VCF file index + pattern: "*.tbi" - versions: type: file description: File containing software versions diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test b/modules/nf-core/bcftools/concat/tests/main.nf.test index bf1a5f3f..cea386e3 100644 --- a/modules/nf-core/bcftools/concat/tests/main.nf.test +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test @@ -9,22 +9,54 @@ nextflow_process { tag "bcftools" tag "bcftools/concat" - config "./nextflow.config" test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]") { + config "./nextflow.config" + when { process { """ - input[0] = [ + input[0] = [ [ id:'test3' ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) ], [ - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) ] ] """ @@ -36,25 +68,33 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.versions - ).match() } + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } ) } } - test("sarscov2 - [[vcf1, vcf2], []]") { + test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" when { process { """ - input[0] = [ + input[0] = [ [ id:'test3' ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) ], - [] + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] ] """ } @@ -65,28 +105,32 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.versions - ).match() } + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } ) } } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub") { + test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" - options "-stub" when { process { """ - input[0] = [ + input[0] = [ [ id:'test3' ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) ], [ - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) ] ] """ @@ -97,12 +141,176 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.vcf[0][1]).name, + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.versions - ).match() } + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + + test("sarscov2 - [[vcf1, vcf2], []]") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } ) } } -} + test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap index 7344e6e3..1182854f 100644 --- a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap @@ -1,43 +1,395 @@ { + "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T08:09:13.734103412" + }, "sarscov2 - [[vcf1, vcf2], []]": { "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + "versions": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T15:19:09.213249578" + }, + "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], [ [ { "id": "test3" }, - "test3.vcf.gz:md5,4bcd0afd89f56c5d433f6b6abc44d0a6" + "test3_vcf.vcf.gz.csi" ] ], [ - "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + + ], + [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" ] ], - "timestamp": "2023-11-29T13:52:27.03724666" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T08:08:23.981388325" + }, + "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T14:01:24.419027693" }, "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]": { "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + "versions": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T15:19:03.597061078" + }, + "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], [ [ { "id": "test3" }, - "test3.vcf.gz:md5,4bcd0afd89f56c5d433f6b6abc44d0a6" + "test3_vcf.vcf.gz.csi" ] ], [ - "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + + ], + [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" ] ], - "timestamp": "2023-11-29T13:52:21.468988293" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T14:00:10.868487669" }, "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub": { "content": [ - "test3.vcf.gz", + { + "0": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T15:19:14.836256897" + }, + "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi": { + "content": [ [ - "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + [ + + ], + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" ] ], - "timestamp": "2023-11-29T13:41:04.716017811" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T14:00:31.061411617" + }, + "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T14:01:35.209746508" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/concat/tests/vcf_gz_index.config b/modules/nf-core/bcftools/concat/tests/vcf_gz_index.config new file mode 100644 index 00000000..7dd696ee --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index --no-version" +} diff --git a/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..aebffb6f --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi --no-version" +} diff --git a/modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..b192ae7d --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi --no-version" +} diff --git a/modules/nf-core/bcftools/pluginscatter/environment.yml b/modules/nf-core/bcftools/pluginscatter/environment.yml index 42e97daa..51bce4d3 100644 --- a/modules/nf-core/bcftools/pluginscatter/environment.yml +++ b/modules/nf-core/bcftools/pluginscatter/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/pluginscatter/main.nf b/modules/nf-core/bcftools/pluginscatter/main.nf index 9f52e947..b3b6691d 100644 --- a/modules/nf-core/bcftools/pluginscatter/main.nf +++ b/modules/nf-core/bcftools/pluginscatter/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_PLUGINSCATTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcf), path(tbi) @@ -17,6 +17,8 @@ process BCFTOOLS_PLUGINSCATTER { output: tuple val(meta), path("*{vcf,vcf.gz,bcf,bcf.gz}") , emit: scatter + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true path "versions.yml" , emit: versions when: @@ -57,11 +59,23 @@ process BCFTOOLS_PLUGINSCATTER { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index_1 = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}0.${extension}.${index}" : "" + def create_index_2 = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}1.${extension}.${index}" : "" + def create_index_3 = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}2.${extension}.${index}" : "" """ - touch ${prefix}1.${extension} - touch ${prefix}2.${extension} - touch ${prefix}3.${extension} + ${create_cmd} ${prefix}0.${extension} + ${create_cmd} ${prefix}1.${extension} + ${create_cmd} ${prefix}2.${extension} + + ${create_index_1} + ${create_index_2} + ${create_index_3} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/pluginscatter/meta.yml b/modules/nf-core/bcftools/pluginscatter/meta.yml index 1a716ead..71805c03 100644 --- a/modules/nf-core/bcftools/pluginscatter/meta.yml +++ b/modules/nf-core/bcftools/pluginscatter/meta.yml @@ -66,6 +66,14 @@ output: type: file description: The resulting files of the scattering pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - csi: + type: file + description: Default VCF file index + pattern: "*.csi" + - tbi: + type: file + description: Alternative VCF file index + pattern: "*.tbi" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test b/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test new file mode 100644 index 00000000..ce66336e --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test @@ -0,0 +1,415 @@ +nextflow_process { + + name "Test Process BCFTOOLS_PLUGINSCATTER" + script "../main.nf" + process "BCFTOOLS_PLUGINSCATTER" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/pluginscatter" + + test("homo_sapiens - sites per chunk") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match("vcf_gz_index") }, + { assert process.out.csi[0][1][0] =~ ".*/test_vcf0.vcf.gz.csi" } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match("vcf_gz_index_csi") }, + { assert process.out.csi[0][1][0] =~ ".*/test_vcf0.vcf.gz.csi" } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match("vcf_gz_index_tbi") }, + { assert process.out.tbi[0][1][0] =~ ".*/test_vcf0.vcf.gz.tbi" } + ) + } + + } + + test("homo_sapiens - scatter") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = "chr21" + input[3] = [] + input[4] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - scatter file") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + input[3] = Channel.of("chr21:6000000-41743940\tfile1", "chr21:41743941-46661900\tfile2") + .collectFile(name:"scatter.tsv", newLine:true) + input[4] = [] + input[5] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - sites per chunk - stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - scatter - stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = "chr21" + input[3] = [] + input[4] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - scatter file - stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + input[3] = Channel.of("chr21:6000000-41743940\tfile1", "chr21:41743941-46661900\tfile2") + .collectFile(name:"scatter.tsv", newLine:true) + input[4] = [] + input[5] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1][0] =~ ".*/test_vcf0.vcf.gz.csi" } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1][0] =~ ".*/test_vcf0.vcf.gz.csi" } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1][0] =~ ".*/test_vcf0.vcf.gz.tbi" } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test.snap new file mode 100644 index 00000000..3168f91b --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test.snap @@ -0,0 +1,623 @@ +{ + "homo_sapiens - 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sites per chunk - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test_vcf0.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_vcf1.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_vcf2.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + [ + { + "id": "test" + }, + [ + "test_vcf0.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_vcf1.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_vcf2.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ], + "csi": [ + + ], + "scatter": [ + [ + { + "id": "test" + }, + [ + "test_vcf0.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_vcf1.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_vcf2.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "tbi": [ + [ + { + "id": "test" + }, + [ + "test_vcf0.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_vcf1.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_vcf2.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T15:10:37.027506409" + }, + "vcf_gz_index": { + "content": [ + [ + + ], + [ + [ + "test_vcf0.vcf.gz.csi", + "test_vcf1.vcf.gz.csi", + "test_vcf2.vcf.gz.csi", + "test_vcf3.vcf.gz.csi", + "test_vcf4.vcf.gz.csi", + "test_vcf5.vcf.gz.csi", + "test_vcf6.vcf.gz.csi", + "test_vcf7.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-06T10:24:46.201810185" + }, + "vcf_gz_index_csi": { + "content": [ + [ + + ], + [ + [ + "test_vcf0.vcf.gz.csi", + "test_vcf1.vcf.gz.csi", + "test_vcf2.vcf.gz.csi", + "test_vcf3.vcf.gz.csi", + "test_vcf4.vcf.gz.csi", + "test_vcf5.vcf.gz.csi", + "test_vcf6.vcf.gz.csi", + "test_vcf7.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-06T10:27:20.636624541" + }, + "homo_sapiens - scatter": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "testchr21.vcf:md5,68e3660b6d619163692edad8ba7dd179" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ], + "csi": [ + + ], + "scatter": [ + [ + { + "id": "test" + }, + "testchr21.vcf:md5,68e3660b6d619163692edad8ba7dd179" + ] + ], + "tbi": [ + + ], + "versions": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T14:40:12.621284696" + }, + "homo_sapiens - sites per chunk - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test0.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test1.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test2.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ], + "csi": [ + + ], + "scatter": [ + [ + { + "id": "test" + }, + [ + "test0.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test1.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test2.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "tbi": [ + + ], + "versions": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T15:08:56.987822348" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/pluginscatter/tests/nextflow.config b/modules/nf-core/bcftools/pluginscatter/tests/nextflow.config new file mode 100644 index 00000000..aa8d093b --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/nextflow.config @@ -0,0 +1,3 @@ +process { + ext.args = '--no-version' +} diff --git a/modules/nf-core/bcftools/pluginscatter/tests/tags.yml b/modules/nf-core/bcftools/pluginscatter/tests/tags.yml new file mode 100644 index 00000000..60cebd43 --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/pluginscatter: + - "modules/nf-core/bcftools/pluginscatter/**" diff --git a/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index.config b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index.config new file mode 100644 index 00000000..7dd696ee --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index --no-version" +} diff --git a/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..aebffb6f --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi --no-version" +} diff --git a/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..b192ae7d --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi --no-version" +} diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml index 89cf911d..2295ecfd 100644 --- a/modules/nf-core/bcftools/sort/environment.yml +++ b/modules/nf-core/bcftools/sort/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index c982944c..7d4c9b8e 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -4,15 +4,17 @@ process BCFTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcf) output: - tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}") , emit: vcf - path "versions.yml" , emit: versions + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -49,9 +51,16 @@ process BCFTOOLS_SORT { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" """ - touch ${prefix}.${extension} + ${create_cmd} ${prefix}.${extension} + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/sort/meta.yml b/modules/nf-core/bcftools/sort/meta.yml index 84747c6d..dfbddcba 100644 --- a/modules/nf-core/bcftools/sort/meta.yml +++ b/modules/nf-core/bcftools/sort/meta.yml @@ -36,6 +36,14 @@ output: type: file description: Sorted VCF file pattern: "*.{vcf.gz}" + - csi: + type: file + description: Default VCF file index + pattern: "*.csi" + - tbi: + type: file + description: Alternative VCF file index + pattern: "*.tbi" authors: - "@Gwennid" maintainers: diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test b/modules/nf-core/bcftools/sort/tests/main.nf.test new file mode 100644 index 00000000..b9bdd76a --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/main.nf.test @@ -0,0 +1,222 @@ +nextflow_process { + + name "Test Process BCFTOOLS_SORT" + script "../main.nf" + process "BCFTOOLS_SORT" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/sort" + + test("sarscov2 - vcf") { + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match("vcf") } + ) + } + + } + + test("sarscov2 - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + test("sarscov2 - vcf - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test.snap b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap new file mode 100644 index 00000000..f38272cb --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap @@ -0,0 +1,350 @@ +{ + "sarscov2 - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:06:05.201680777" + }, + "vcf": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "versions": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:04:43.889971134" + }, + "sarscov2 - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:04:55.385964497" + }, + "sarscov2 - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:05:06.662818922" + }, + "sarscov2 - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ], + "csi": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:05:40.012912381" + }, + "sarscov2 - vcf_gz_index_csi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ], + "csi": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:05:52.405673587" + }, + "sarscov2 - vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:05:29.117946461" + }, + "sarscov2 - vcf_gz_index_tbi": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + + ], + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:05:17.217274984" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/sort/tests/tags.yml b/modules/nf-core/bcftools/sort/tests/tags.yml new file mode 100644 index 00000000..6e9520dd --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/sort: + - "modules/nf-core/bcftools/sort/**" diff --git a/modules/nf-core/bcftools/sort/tests/vcf_gz_index.config b/modules/nf-core/bcftools/sort/tests/vcf_gz_index.config new file mode 100644 index 00000000..aacd1346 --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index" +} diff --git a/modules/nf-core/bcftools/sort/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/sort/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..640eb0ba --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi" +} diff --git a/modules/nf-core/bcftools/sort/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/sort/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..589a50c6 --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi" +} diff --git a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff deleted file mode 100644 index 63309f0b..00000000 --- a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff +++ /dev/null @@ -1,38 +0,0 @@ -Changes in module 'nf-core/ensemblvep/vep' ---- modules/nf-core/ensemblvep/vep/main.nf -+++ modules/nf-core/ensemblvep/vep/main.nf -@@ -2,10 +2,10 @@ - tag "$meta.id" - label 'process_medium' - -- conda "bioconda::ensembl-vep=109.3" -+ conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'https://depot.galaxyproject.org/singularity/ensembl-vep:109.3--pl5321h2a3209d_1' : -- 'biocontainers/ensembl-vep:109.3--pl5321h2a3209d_1' }" -+ 'https://depot.galaxyproject.org/singularity/ensembl-vep:105.0--pl5321h4a94de4_1' : -+ 'biocontainers/ensembl-vep:105.0--pl5321h4a94de4_1' }" - - input: - tuple val(meta), path(vcf), path(custom_extra_files) -@@ -48,7 +48,6 @@ - --fork $task.cpus \\ - --stats_file ${prefix}.summary.html \\ - -- - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') - ---- /dev/null -+++ modules/nf-core/ensemblvep/vep/environment.yml -@@ -0,0 +1,7 @@ -+name: ensemblvep_download -+channels: -+ - conda-forge -+ - bioconda -+ - defaults -+dependencies: -+ - bioconda::ensembl-vep=105.0 - -************************************************************ diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml index adba76e8..3eae4fb1 100644 --- a/modules/nf-core/ensemblvep/vep/environment.yml +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -1,7 +1,7 @@ -name: ensemblvep_download +name: ensemblvep_vep channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::ensembl-vep=105.0 + - bioconda::ensembl-vep=112.0 diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index 65fbd53d..5f33265b 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -4,8 +4,8 @@ process ENSEMBLVEP_VEP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:105.0--pl5321h4a94de4_1' : - 'biocontainers/ensembl-vep:105.0--pl5321h4a94de4_1' }" + 'https://depot.galaxyproject.org/singularity/ensembl-vep:112.0--pl5321h2a3209d_0' : + 'biocontainers/ensembl-vep:112.0--pl5321h2a3209d_0' }" input: tuple val(meta), path(vcf), path(custom_extra_files) @@ -20,7 +20,7 @@ process ENSEMBLVEP_VEP { tuple val(meta), path("*.vcf.gz") , optional:true, emit: vcf tuple val(meta), path("*.tab.gz") , optional:true, emit: tab tuple val(meta), path("*.json.gz") , optional:true, emit: json - path "*.summary.html" , emit: report + path "*.html" , optional:true, emit: report path "versions.yml" , emit: versions when: @@ -45,8 +45,8 @@ process ENSEMBLVEP_VEP { --cache \\ --cache_version $cache_version \\ --dir_cache $dir_cache \\ - --fork $task.cpus \\ - --stats_file ${prefix}.summary.html \\ + --fork $task.cpus + cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -57,10 +57,10 @@ process ENSEMBLVEP_VEP { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf.gz - touch ${prefix}.tab.gz - touch ${prefix}.json.gz - touch ${prefix}.summary.html + echo "" | gzip > ${prefix}.vcf.gz + echo "" | gzip > ${prefix}.tab.gz + echo "" | gzip > ${prefix}.json.gz + touch ${prefix}_summary.html cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml index 7783847d..d8ff8d14 100644 --- a/modules/nf-core/ensemblvep/vep/meta.yml +++ b/modules/nf-core/ensemblvep/vep/meta.yml @@ -1,4 +1,4 @@ -name: ENSEMBLVEP_VEP +name: ensemblvep_vep description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`. keywords: - annotation @@ -86,3 +86,7 @@ authors: - "@maxulysse" - "@matthdsm" - "@nvnieuwk" +maintainers: + - "@maxulysse" + - "@matthdsm" + - "@nvnieuwk" diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test new file mode 100644 index 00000000..e68fff3c --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test @@ -0,0 +1,114 @@ +nextflow_process { + + name "Test Process ENSEMBLVEP_VEP" + script "../main.nf" + process "ENSEMBLVEP_VEP" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "ensemblvep" + tag "ensemblvep/vep" + tag "ensemblvep/download" + + test("test_ensemblvep_vep_fasta_vcf") { + config "./vcf.config" + + setup { + run("ENSEMBLVEP_DOWNLOAD") { + script "../../download/main.nf" + + process { + """ + input[0] = Channel.of([ + [id:"112_WBcel235"], + params.vep_genome, + params.vep_species, + params.vep_cache_version + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] + ]) + input[1] = params.vep_genome + input[2] = params.vep_species + input[3] = params.vep_cache_version + input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] } + input[5] = Channel.value([ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[6] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") } + ) + } + + } + + test("test_ensemblvep_vep_fasta_tab_gz") { + config "./tab.gz.config" + + setup { + run("ENSEMBLVEP_DOWNLOAD") { + script "../../download/main.nf" + + process { + """ + input[0] = Channel.of([ + [id:"112_WBcel235"], + params.vep_genome, + params.vep_species, + params.vep_cache_version + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] + ]) + input[1] = params.vep_genome + input[2] = params.vep_species + input[3] = params.vep_cache_version + input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] } + input[5] = Channel.value([ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[6] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + { assert path(process.out.tab.get(0).get(1)).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v112.0") } + ) + } + } +} diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap new file mode 100644 index 00000000..1c4c0e4e --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap @@ -0,0 +1,26 @@ +{ + "test_ensemblvep_vep_fasta_tab_gz": { + "content": [ + [ + "versions.yml:md5,d06f1eb60f534489026d682eb3aa5559" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-02T10:15:18.228927" + }, + "test_ensemblvep_vep_fasta_vcf": { + "content": [ + [ + "versions.yml:md5,d06f1eb60f534489026d682eb3aa5559" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-02T10:14:50.193861" + } +} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/vep/tests/nextflow.config b/modules/nf-core/ensemblvep/vep/tests/nextflow.config new file mode 100644 index 00000000..9aa48164 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/nextflow.config @@ -0,0 +1,12 @@ +params { + vep_cache_version = "112" + vep_genome = "WBcel235" + vep_species = "caenorhabditis_elegans" +} + +process { + withName: ENSEMBLVEP_DOWNLOAD { + ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' + ext.prefix = { "${params.vep_cache_version}_${params.vep_genome}" } + } +} diff --git a/modules/nf-core/ensemblvep/vep/tests/tab.gz.config b/modules/nf-core/ensemblvep/vep/tests/tab.gz.config new file mode 100644 index 00000000..40eb03e5 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/tab.gz.config @@ -0,0 +1,5 @@ +process { + withName: ENSEMBLVEP_VEP { + ext.args = '--tab --compress_output bgzip' + } +} diff --git a/modules/nf-core/ensemblvep/vep/tests/tags.yml b/modules/nf-core/ensemblvep/vep/tests/tags.yml new file mode 100644 index 00000000..4aa4aa45 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/tags.yml @@ -0,0 +1,2 @@ +ensemblvep/vep: + - "modules/nf-core/ensemblvep/vep/**" diff --git a/modules/nf-core/ensemblvep/vep/tests/vcf.config b/modules/nf-core/ensemblvep/vep/tests/vcf.config new file mode 100644 index 00000000..ad8955a3 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/vcf.config @@ -0,0 +1,5 @@ +process { + withName: ENSEMBLVEP_VEP { + ext.args = '--vcf' + } +} diff --git a/modules/nf-core/happy/happy/environment.yml b/modules/nf-core/happy/happy/environment.yml deleted file mode 100644 index 3d29dcb2..00000000 --- a/modules/nf-core/happy/happy/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: happy_happy -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::hap.py=0.3.14 diff --git a/modules/nf-core/happy/happy/main.nf b/modules/nf-core/happy/happy/main.nf deleted file mode 100644 index b3cc12d5..00000000 --- a/modules/nf-core/happy/happy/main.nf +++ /dev/null @@ -1,84 +0,0 @@ -process HAPPY_HAPPY { - tag "$meta.id" - label 'process_medium' - - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0': - 'biocontainers/hap.py:0.3.14--py27h5c5a3ab_0' }" - - input: - tuple val(meta), path(query_vcf), path(truth_vcf), path(regions_bed), path(targets_bed) - tuple val(meta2), path(fasta) - tuple val(meta3), path(fasta_fai) - tuple val(meta4), path(false_positives_bed) - tuple val(meta5), path(stratification_tsv) - tuple val(meta6), path(stratification_beds) - - output: - tuple val(meta), path('*.summary.csv') , emit: summary_csv - tuple val(meta), path('*.roc.all.csv.gz') , emit: roc_all_csv - tuple val(meta), path('*.roc.Locations.INDEL.csv.gz') , emit: roc_indel_locations_csv - tuple val(meta), path('*.roc.Locations.INDEL.PASS.csv.gz') , emit: roc_indel_locations_pass_csv - tuple val(meta), path('*.roc.Locations.SNP.csv.gz') , emit: roc_snp_locations_csv - tuple val(meta), path('*.roc.Locations.SNP.PASS.csv.gz') , emit: roc_snp_locations_pass_csv - tuple val(meta), path('*.extended.csv') , emit: extended_csv - tuple val(meta), path('*.runinfo.json') , emit: runinfo - tuple val(meta), path('*.metrics.json.gz') , emit: metrics_json - tuple val(meta), path('*.vcf.gz') , emit: vcf, optional:true - tuple val(meta), path('*.tbi') , emit: tbi, optional:true - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def regions = regions_bed ? "-R ${regions_bed}" : "" - def targets = targets_bed ? "-T ${targets_bed}" : "" - def false_positives = false_positives_bed ? "--false-positives ${false_positives_bed}" : "" - def stratification = stratification_tsv ? "--stratification ${stratification_tsv}" : "" - def VERSION = '0.3.14' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - """ - hap.py \\ - ${truth_vcf} \\ - ${query_vcf} \\ - ${args} \\ - --reference ${fasta} \\ - --threads ${task.cpus} \\ - ${regions} \\ - ${targets} \\ - ${false_positives} \\ - ${stratification} \\ - -o ${prefix} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hap.py: $VERSION - END_VERSIONS - """ - - stub: - def args = task.ext.args ?: '' - def VERSION = '0.3.14' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - """ - touch ${prefix}.summary.csv - touch ${prefix}.roc.all.csv.gz - touch ${prefix}.roc.Locations.INDEL.csv.gz - touch ${prefix}.roc.Locations.INDEL.PASS.csv.gz - touch ${prefix}.roc.Locations.SNP.csv.gz - touch ${prefix}.roc.Locations.SNP.PASS.csv.gz - touch ${prefix}.extended.csv - touch ${prefix}.runinfo.json - touch ${prefix}.metrics.json.gz - touch ${prefix}.vcf.gz - touch ${prefix}.vcf.gz.tbi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hap.py: $VERSION - END_VERSIONS - """ -} diff --git a/modules/nf-core/happy/happy/meta.yml b/modules/nf-core/happy/happy/meta.yml deleted file mode 100644 index 85912cb5..00000000 --- a/modules/nf-core/happy/happy/meta.yml +++ /dev/null @@ -1,114 +0,0 @@ -name: "happy_happy" -description: Hap.py is a tool to compare diploid genotypes at haplotype level. Rather than comparing VCF records row by row, hap.py will generate and match alternate sequences in a superlocus. A superlocus is a small region of the genome (sized between 1 and around 1000 bp) that contains one or more variants. -keywords: - - happy - - benchmark - - haplotype - - validation -tools: - - "happy": - description: "Haplotype VCF comparison tools" - homepage: "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html" - documentation: "https://github.com/Illumina/hap.py" - tool_dev_url: "https://github.com/Illumina/hap.py" - licence: "['BSD-2-clause']" -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - query_vcf: - type: file - description: VCF/GVCF file to query - pattern: "*.{gvcf,vcf}.gz" - - truth_vcf: - type: file - description: gold standard VCF file - pattern: "*.{gvcf,vcf}.gz" - - regions_bed: - type: file - description: Sparse regions to restrict the analysis to - pattern: "*.bed" - - targets_bed: - type: file - description: Dense regions to restrict the analysis to - pattern: "*.bed" - - fasta: - type: file - description: FASTA file of the reference genome - pattern: "*.{fa,fasta}" - - fasta_fai: - type: file - description: The index of the reference FASTA - pattern: "*.fai" - - false_positives_bed: - type: file - description: False positive / confident call regions. Calls outside these regions will be labelled as UNK. - pattern: "*.{bed,bed.gz}" - - stratification_tsv: - type: file - description: Stratification file list in TSV format - pattern: "*.tsv" - - stratification_beds: - type: file(s) - description: One or more BED files used for stratification (these should be referenced in the stratification TSV) - pattern: "*.bed" -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - summary_csv: - type: file - description: A CSV file containing the summary of the benchmarking - pattern: "*.summary.csv" - - roc_all_csv: - type: file - description: A CSV file containing ROC values for all variants - pattern: "*.roc.all.csv.gz" - - roc_indel_locations_csv: - type: file - description: A CSV file containing ROC values for all indels - pattern: "*.roc.Locations.INDEL.csv.gz" - - roc_indel_locations_pass_csv: - type: file - description: A CSV file containing ROC values for all indels that passed all filters - pattern: "*.roc.Locations.INDEL.PASS.csv.gz" - - roc_snp_locations_csv: - type: file - description: A CSV file containing ROC values for all SNPs - pattern: "*.roc.Locations.SNP.csv.gz" - - roc_snp_locations_pass_csv: - type: file - description: A CSV file containing ROC values for all SNPs that passed all filters - pattern: "*.roc.Locations.SNP.PASS.csv.gz" - - extended_csv: - type: file - description: A CSV file containing extended info of the benchmarking - pattern: "*.extended.csv" - - json: - type: file - description: A JSON file containing the run info - pattern: "*.runinfo.json" - - runinfo: - type: file - description: A JSON file containing the benchmarking metrics - pattern: "*.metrics.json.gz" - - vcf: - type: file - description: An annotated VCF - pattern: "*.vcf.gz" - - tbi: - type: file - description: The index of the annotated VCF - pattern: "*.tbi" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@nvnieuwk" -maintainers: - - "@nvnieuwk" diff --git a/modules/nf-core/snpeff/snpeff/main.nf b/modules/nf-core/snpeff/snpeff/main.nf index cc4f2ccb..28d13826 100644 --- a/modules/nf-core/snpeff/snpeff/main.nf +++ b/modules/nf-core/snpeff/snpeff/main.nf @@ -13,11 +13,11 @@ process SNPEFF_SNPEFF { tuple val(meta2), path(cache) output: - tuple val(meta), path("*.ann.vcf"), emit: vcf - path "*.csv" , emit: report - path "*.html" , emit: summary_html - path "*.genes.txt" , emit: genes_txt - path "versions.yml" , emit: versions + tuple val(meta), path("*.ann.vcf"), emit: vcf + tuple val(meta), path("*.csv"), emit: report + tuple val(meta), path("*.html"), emit: summary_html + tuple val(meta), path("*.genes.txt"), emit: genes_txt + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/snpeff/snpeff/tests/main.nf.test b/modules/nf-core/snpeff/snpeff/tests/main.nf.test new file mode 100644 index 00000000..803ff02c --- /dev/null +++ b/modules/nf-core/snpeff/snpeff/tests/main.nf.test @@ -0,0 +1,51 @@ +nextflow_process { + + name "Test Process SNPEFF_SNPEFF" + script "../main.nf" + process "SNPEFF_SNPEFF" + config "./nextflow.config" + tag "modules" + tag "modules_nfcore" + tag "modules_snpeff" + tag "snpeff" + tag "snpeff/download" + tag "snpeff/snpeff" + + test("test_SNPEFF_SNPEFF") { + + setup { + run("SNPEFF_DOWNLOAD") { + script "../../download/main.nf" + process { + """ + input[0] = Channel.of([[id:params.snpeff_genome + '.' + params.snpeff_cache_version], params.snpeff_genome, params.snpeff_cache_version]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ]) + input[1] = params.snpeff_genome + '.' + params.snpeff_cache_version + input[2] = SNPEFF_DOWNLOAD.out.cache + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.report[0][1]).exists() }, + { assert path(process.out.summary_html[0][1]).exists() }, + { assert path(process.out.vcf[0][1]).exists() }, + { assert snapshot(process.out.genes_txt).match("genes_txt") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } +} diff --git a/modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap b/modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap new file mode 100644 index 00000000..0891b844 --- /dev/null +++ b/modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap @@ -0,0 +1,31 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,25d44a118d558b331d51ec00be0d997c" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.02.0" + }, + "timestamp": "2024-03-18T17:37:18.879477" + }, + "genes_txt": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.genes.txt:md5,130536bf0237d7f3f746d32aaa32840a" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.02.0" + }, + "timestamp": "2024-03-18T17:37:18.874822" + } +} \ No newline at end of file diff --git a/modules/nf-core/snpeff/snpeff/tests/nextflow.config b/modules/nf-core/snpeff/snpeff/tests/nextflow.config new file mode 100644 index 00000000..d31ebf6b --- /dev/null +++ b/modules/nf-core/snpeff/snpeff/tests/nextflow.config @@ -0,0 +1,4 @@ +params { + snpeff_cache_version = "105" + snpeff_genome = "WBcel235" +} diff --git a/modules/nf-core/snpeff/snpeff/tests/tags.yml b/modules/nf-core/snpeff/snpeff/tests/tags.yml new file mode 100644 index 00000000..427b588d --- /dev/null +++ b/modules/nf-core/snpeff/snpeff/tests/tags.yml @@ -0,0 +1,2 @@ +snpeff/snpeff: + - "modules/nf-core/snpeff/snpeff/**" diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index 7167fb87..4d1f9dd4 100644 --- a/modules/nf-core/tabix/tabix/environment.yml +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -1,7 +1,10 @@ name: tabix_tabix + channels: - conda-forge - bioconda - defaults + dependencies: + - bioconda::htslib=1.20 - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index c304a8a3..13acd670 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -4,8 +4,8 @@ process TABIX_TABIX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'biocontainers/tabix:1.11--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : + 'biocontainers/htslib:1.20--h5efdd21_2' }" input: tuple val(meta), path(tab) @@ -21,7 +21,10 @@ process TABIX_TABIX { script: def args = task.ext.args ?: '' """ - tabix $args $tab + tabix \\ + --threads $task.cpus \\ + $args \\ + $tab cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -30,11 +33,11 @@ process TABIX_TABIX { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${tab}.tbi - cat <<-END_VERSIONS > versions.yml + touch ${tab}.csi + cat <<-END_VERSIONS > versions.yml "${task.process}": tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test new file mode 100644 index 00000000..102b0d7b --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test @@ -0,0 +1,136 @@ +nextflow_process { + + name "Test Process TABIX_TABIX" + script "modules/nf-core/tabix/tabix/main.nf" + process "TABIX_TABIX" + + tag "modules" + tag "modules_nfcore" + tag "tabix" + tag "tabix/tabix" + + test("sarscov2_bedgz_tbi") { + config "./tabix_bed.config" + when { + process { + """ + input[0] = [ + [ id:'tbi_bed' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.tbi[0][1]).name + ).match() } + ) + } + } + + test("sarscov2_gff_tbi") { + config "./tabix_gff.config" + when { + process { + """ + input[0] = [ + [ id:'tbi_gff' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.tbi[0][1]).name).match() } + ) + } + + } + + test("sarscov2_vcf_tbi") { + config "./tabix_vcf_tbi.config" + when { + process { + """ + input[0] = [ + [ id:'tbi_vcf' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.tbi[0][1]).name + ).match() } + ) + } + + } + + test("sarscov2_vcf_csi") { + config "./tabix_vcf_csi.config" + when { + process { + """ + input[0] = [ + [ id:'vcf_csi' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.csi[0][1]).name + ).match() } + ) + } + + } + + test("sarscov2_vcf_csi_stub") { + config "./tabix_vcf_csi.config" + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'vcf_csi_stub' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.csi[0][1]).name + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap new file mode 100644 index 00000000..c2b9ed0b --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap @@ -0,0 +1,212 @@ +{ + "sarscov2_gff_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_gff" + }, + "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "tbi_gff" + }, + "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926" + ] + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "genome.gff3.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:25.653807564" + }, + "sarscov2_bedgz_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_bed" + }, + "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "tbi_bed" + }, + "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d" + ] + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "test.bed.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:09.754082161" + }, + "sarscov2_vcf_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_vcf" + }, + "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "tbi_vcf" + }, + "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e" + ] + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "test.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:40.042648294" + }, + "sarscov2_vcf_csi_stub": { + "content": [ + { + "0": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "test.vcf.gz.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:07:08.700367261" + }, + "sarscov2_vcf_csi": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "vcf_csi" + }, + "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b" + ] + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + [ + { + "id": "vcf_csi" + }, + "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b" + ] + ], + "tbi": [ + + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "test.vcf.gz.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:55.362067748" + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_bed.config b/modules/nf-core/tabix/tabix/tests/tabix_bed.config new file mode 100644 index 00000000..7ff05905 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_bed.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p bed' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_gff.config b/modules/nf-core/tabix/tabix/tests/tabix_gff.config new file mode 100644 index 00000000..20c0a1e3 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_gff.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p gff' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config new file mode 100644 index 00000000..eb4f2d7e --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p vcf --csi' + } +} diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config new file mode 100644 index 00000000..2774c8a9 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p vcf' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tags.yml b/modules/nf-core/tabix/tabix/tests/tags.yml new file mode 100644 index 00000000..6eda0653 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tags.yml @@ -0,0 +1,2 @@ +tabix/tabix: + - "modules/nf-core/tabix/tabix/**" diff --git a/modules/nf-core/vcf2db/vcf2db.diff b/modules/nf-core/vcf2db/vcf2db.diff deleted file mode 100644 index 00fc493f..00000000 --- a/modules/nf-core/vcf2db/vcf2db.diff +++ /dev/null @@ -1,143 +0,0 @@ -Changes in module 'nf-core/vcf2db' ---- modules/nf-core/vcf2db/main.nf -+++ modules/nf-core/vcf2db/main.nf -@@ -4,9 +4,7 @@ - - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "${moduleDir}/environment.yml" -- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'https://depot.galaxyproject.org/singularity/vcf2db:2020.02.24--pl5321hdfd78af_3': -- 'biocontainers/vcf2db:2020.02.24--pl5321hdfd78af_3' }" -+ container "cmgg/vcf2db:2020.02.24" - - input: - tuple val(meta), path(vcf), path(ped) -@@ -29,6 +27,12 @@ - ${prefix}.db \\ - $args - -+ sqlite3 ${prefix}.db 'CREATE INDEX idx_variant_impacts_id ON variant_impacts (variant_id)' && \\ -+ sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN tags varchar(255)' && \\ -+ sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN tags_user varchar(255)' && \\ -+ sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN notes varchar(255)' && \\ -+ sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN notes_user varchar(255)' -+ - cat <<-END_VERSIONS > versions.yml - "${task.process}": - vcf2db: $VERSION - ---- /dev/null -+++ modules/nf-core/vcf2db/vcf2db_env.yaml -@@ -0,0 +1,96 @@ -+name: base -+channels: -+ - conda-forge -+ - bioconda -+ - defaults -+dependencies: -+ - _libgcc_mutex=0.1=conda_forge -+ - _openmp_mutex=4.5=1_llvm -+ - backports=1.0=py27_1 -+ - backports.functools_lru_cache=1.6.1=pyhd3eb1b0_0 -+ - backports.shutil_get_terminal_size=1.0.0=py27_2 -+ - backports_abc=0.5=py27_0 -+ - backports.functools_lru_cache=1.6.1=pyhd3eb1b0_0 -+ - backports_abc=0.5=py27_0 -+ - blas=2.17=openblas -+ - bzip2=1.0.8=h516909a_3 -+ - c-ares=1.17.1=h36c2ea0_0 -+ - ca-certificates=2020.11.8=ha878542_0 -+ - certifi=2016.9.26=py27_0 -+ - click=7.1.2=pyh9f0ad1d_0 -+ - coloredlogs=14.0=py27h8c360ce_1 -+ - cycler=0.10.0=py27_0 -+ - cyvcf2=0.20.9=py27h22a6d1c_0 -+ - decorator=4.4.2=py_0 -+ - freetype=2.10.4=he06d7ca_0 -+ - functools32=3.2.3.2=py27_2 -+ - futures=3.3.0=py27h8c360ce_1 -+ - geneimpacts=0.3.7=py27_0 -+ - htslib=1.10.2=hd3b49d5_1 -+ - humanfriendly=8.1=py27h8c360ce_1 -+ - icu=58.2=hf484d3e_1000 -+ - kiwisolver=1.1.0=py27h9e3301b_1 -+ - krb5=1.17.2=h926e7f8_0 -+ - libblas=3.8.0=17_openblas -+ - libcblas=3.8.0=17_openblas -+ - libcurl=7.71.1=hcdd3856_8 -+ - libdeflate=1.6=h516909a_0 -+ - libedit=3.1.20191231=he28a2e2_2 -+ - libev=4.33=h516909a_1 -+ - libffi=3.3=he6710b0_2 -+ - libgcc-ng=9.3.0=h5dbcf3e_17 -+ - libgfortran-ng=7.5.0=hae1eefd_17 -+ - libgfortran4=7.5.0=hae1eefd_17 -+ - liblapack=3.8.0=17_openblas -+ - liblapacke=3.8.0=17_openblas -+ - liblapacke=3.8.0=17_openblas -+ - libnghttp2=1.41.0=hf8bcb03_2 -+ - libopenblas=0.3.10=pthreads_hb3c22a3_5 -+ - libpng=1.6.37=hed695b0_2 -+ - libssh2=1.9.0=hab1572f_5 -+ - libstdcxx-ng=9.3.0=h2ae2ef3_17 -+ - llvm-openmp=11.0.0=hfc4b9b4_1 -+ - matplotlib-base=2.2.4=py27hfd891ef_0 -+ - monotonic=1.5=py_0 -+ - ncurses=6.2=h58526e2_4 -+ - networkx=2.2=py27_1 -+ - nomkl=3.0=0 -+ - numpy=1.16.6=py27h30dfecb_0 -+ - numpy-base=1.16.6=py27h2f8d375_0 -+ - numpy-base=1.16.6=py27h2f8d375_0 -+ - openssl=1.1.1h=h516909a_0 -+ - pandas=0.24.2=py27hf484d3e_0 -+ - pathlib2=2.3.5=py27h8c360ce_1 -+ - patsy=0.5.1=py27_0 -+ - peddy=0.4.7=pyh864c0ab_0 -+ - pip=20.1.1=pyh9f0ad1d_0 -+ - pyparsing=2.4.7=pyh9f0ad1d_0 -+ - python=2.7.18=h15b4118_1 -+ - python-dateutil=2.8.1=py_0 -+ - python-lzo=1.12=py27h42e1302_1001 -+ - python-snappy=0.5.4=py27hee44bf9_1 -+ - python_abi=2.7=1_cp27mu -+ - python-dateutil=2.8.1=py_0 -+ - python-snappy=0.5.4=py27hee44bf9_1 -+ - python_abi=2.7=1_cp27mu -+ - pytz=2020.1=pyh9f0ad1d_0 -+ - readline=8.0=he28a2e2_2 -+ - scandir=1.10.0=py27hdf8410d_1 -+ - scikit-learn=0.20.3=py27ha8026db_1 -+ - scipy=1.2.1=py27h921218d_2 -+ - seaborn=0.9.0=py27_0 -+ - setuptools=44.0.0=py27_0 -+ - singledispatch=3.4.0.3=py27_1000 -+ - six=1.15.0=pyh9f0ad1d_0 -+ - snappy=1.1.8=he1b5a44_3 -+ - sqlalchemy=1.3.15=py27hdf8410d_1 -+ - sqlite=3.33.0=h4cf870e_1 -+ - statsmodels=0.10.2=py27hc1659b7_0 -+ - subprocess32=3.5.4=py27h516909a_0 -+ - tk=8.6.10=hed695b0_1 -+ - toolshed=0.4.6=py27_0 -+ - tornado=5.1.1=py27h14c3975_1000 -+ - wheel=0.35.1=pyh9f0ad1d_0 -+ - xz=5.2.5=h516909a_1 -+ - zlib=1.2.11=h516909a_1010 -+ - zstd=1.4.5=h6597ccf_2 - ---- /dev/null -+++ modules/nf-core/vcf2db/Dockerfile -@@ -0,0 +1,11 @@ -+FROM mambaorg/micromamba:1.4-focal -+ -+COPY ./vcf2db_env.yaml . -+ -+RUN micromamba update --file ./vcf2db_env.yaml --yes -+RUN micromamba install --yes --name base --no-deps -c bioconda vcf2db==2020.02.24 -+RUN micromamba install --yes --name base --no-deps -c conda-forge coreutils -+RUN micromamba clean --all --yes -+ -+ARG MAMBA_DOCKERFILE_ACTIVATE=1 -+ENV PATH "$MAMBA_ROOT_PREFIX/bin:$PATH" -************************************************************ From 58e75ef92371a039447390213894d55f1d4d8f40 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 3 Sep 2024 17:52:19 +0200 Subject: [PATCH 13/49] resolve all non module linting issues --- .github/workflows/linting.yml | 14 +- .github/workflows/linting_comment.yml | 2 +- .nf-core.yml | 48 +++-- README.md | 2 +- conf/test_full.config | 4 +- main.nf | 2 +- nextflow.config | 3 +- nextflow_schema.json | 10 +- .../local/vcf_validate_small_variants/main.nf | 171 +++++++----------- workflows/germline.nf | 6 +- 10 files changed, 111 insertions(+), 151 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 49fb4340..7d4ad177 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,6 +1,6 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure +# It runs the `nf-core pipelines lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: push: @@ -41,17 +41,23 @@ jobs: python-version: "3.12" architecture: "x64" + - name: read .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.0.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yaml + - name: Install dependencies run: | python -m pip install --upgrade pip - pip install git+https://github.com/nf-core/tools@dev + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - - name: Run nf-core lint + - name: Run nf-core pipelines lint env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Save PR number if: ${{ always() }} diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 40acc23f..42e519bf 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 + uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.nf-core.yml b/.nf-core.yml index 70105d4f..7c0e227a 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,22 +1,34 @@ lint: - files_exist: - - CODE_OF_CONDUCT.md - - assets/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_dark.png - - .github/ISSUE_TEMPLATE/config.yml - - .github/workflows/awstest.yml - - .github/workflows/awsfulltest.yml - - docs/README.md - files_unchanged: - - CODE_OF_CONDUCT.md - - assets/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_dark.png - - .github/ISSUE_TEMPLATE/bug_report.yml - nextflow_config: - - "custom_config" -nf_core_version: 2.14.1 + files_exist: + - "CODE_OF_CONDUCT.md" + - "assets/nf-core-germline_logo_light.png" + - "docs/images/nf-core-germline_logo_light.png" + - "docs/images/nf-core-germline_logo_dark.png" + - ".github/ISSUE_TEMPLATE/config.yml" + - ".github/workflows/awstest.yml" + - ".github/workflows/awsfulltest.yml" + - "docs/README.md" + files_unchanged: + - ".github/CONTRIBUTING.md" + - ".github/PULL_REQUEST_TEMPLATE.md" + - ".github/workflows/linting_comment.yml" + - ".github/linting.yml" + - "CODE_OF_CONDUCT.md" + - ".github/ISSUE_TEMPLATE/bug_report.yml" + - ".prettierignore" + nextflow_config: + - "custom_config" # TODO Remove this once the new methods are supported + - "manifest.name" + - "manifest.homePage" + - "params.genomes" + - "validation.help.beforeText" + - "validation.help.afterText" + - "validation.summary.beforeText" + - "validation.summary.afterText" + multiqc_config: + - "report_comment" + actions_ci: false # TODO readd this once the linting doesn't act up +nf_core_version: 3.0.0dev repository_type: pipeline template: author: nvnieuwk diff --git a/README.md b/README.md index ed28ef68..bd133931 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![GitHub Actions Linting Status](https://github.com/nf-cmgg/germline/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/germline/actions/workflows/linting.yml) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/conf/test_full.config b/conf/test_full.config index 9943a39d..37b1a6c0 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -15,9 +15,7 @@ params { config_profile_description = 'Full test dataset to check pipeline function' // Input data for full size test - // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) - // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' + // input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' // Genome references genome = 'R64-1-1' diff --git a/main.nf b/main.nf index b64b8d83..988afc56 100644 --- a/main.nf +++ b/main.nf @@ -194,7 +194,7 @@ workflow { def multiqc_logo = params.multiqc_logo ?: "$projectDir/assets/CMGG_logo.png" - + print(params.genomes) // // SUBWORKFLOW: Run initialisation tasks // diff --git a/nextflow.config b/nextflow.config index 12e7effa..46e627fa 100644 --- a/nextflow.config +++ b/nextflow.config @@ -78,9 +78,8 @@ params { // References cmgg_config_base = "/conf/" igenomes_base = null //'s3://ngi-igenomes/igenomes' - igenomes_ignore = true + igenomes_ignore = false genome = "GRCh38" - genomes = [:] genomes_base = "/references/" genomes_ignore = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 34ed7abd..0fc6f59f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -2,7 +2,7 @@ "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-cmgg/germline/master/nextflow_schema.json", "title": "nf-cmgg/germline pipeline parameters", - "description": "A nextflow pipeline for calling and annotating variants", + "description": "A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data", "type": "object", "$defs": { "input_output_options": { @@ -126,13 +126,7 @@ "description": "Do not load the iGenomes reference config.", "fa_icon": "fas fa-ban", "hidden": true, - "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.", - "default": true - }, - "genomes": { - "type": "object", - "description": "A map structure containing the paths to all genome references", - "hidden": true + "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." } }, "required": ["fasta"] diff --git a/subworkflows/local/vcf_validate_small_variants/main.nf b/subworkflows/local/vcf_validate_small_variants/main.nf index 71432d38..eaa17579 100644 --- a/subworkflows/local/vcf_validate_small_variants/main.nf +++ b/subworkflows/local/vcf_validate_small_variants/main.nf @@ -1,6 +1,5 @@ include { RTGTOOLS_VCFEVAL } from '../../../modules/nf-core/rtgtools/vcfeval/main' include { RTGTOOLS_ROCPLOT } from '../../../modules/nf-core/rtgtools/rocplot/main' -include { HAPPY_HAPPY } from '../../../modules/nf-core/happy/happy/main' workflow VCF_VALIDATE_SMALL_VARIANTS { @@ -10,10 +9,6 @@ workflow VCF_VALIDATE_SMALL_VARIANTS { ch_fasta // [happy only] channel: [ meta, fasta ] ch_fasta_fai // [happy only] channel: [ meta, fasta_fai ] ch_vcfeval_sdf // [vcfeval only] channel: [ meta, sdf ] - ch_happy_false_positive_regions // [optional] channel: [ meta, false_positives_bed ] - ch_happy_stratification_tsv // [optional] channel: [ meta, stratification_tsv ] - ch_happy_stratification_beds // [optional] channel: [ meta, [stratification_beds] ] - tools // [mandatory] value: A comma-delimited list of the tools to use for validation (happy,vcfeval,jaccard) main: @@ -51,116 +46,76 @@ workflow VCF_VALIDATE_SMALL_VARIANTS { rtgtools_non_snp_svg_rocplot = Channel.empty() rtgtools_weighted_svg_rocplot = Channel.empty() - val_list_tools = tools.tokenize(",") - ch_input = ch_vcf.join(ch_beds, failOnDuplicate: true, failOnMismatch: true) - if("happy" in val_list_tools){ - ch_happy_input = ch_input - .map { meta, vcf, tbi, truth_vcf, truth_tbi, regions_bed, targets_bed -> - [ meta, vcf, truth_vcf, regions_bed, targets_bed ] + RTGTOOLS_VCFEVAL( + ch_input, + ch_vcfeval_sdf + ) + ch_versions = ch_versions.mix(RTGTOOLS_VCFEVAL.out.versions.first()) + + ch_rocplot_input = RTGTOOLS_VCFEVAL.out.snp_roc + .map { meta, tsv -> + [ meta + [roc_type:'snp'], tsv ] + } + .mix( + RTGTOOLS_VCFEVAL.out.non_snp_roc.map { meta, tsv -> + [ meta + [roc_type:'non_snp'], tsv ] + }, + RTGTOOLS_VCFEVAL.out.weighted_roc.map { meta, tsv -> + [ meta + [roc_type:'weighted'], tsv ] } - HAPPY_HAPPY ( - ch_happy_input, - ch_fasta, - ch_fasta_fai, - ch_happy_false_positive_regions, - ch_happy_stratification_tsv, - ch_happy_stratification_beds - ) - ch_versions = ch_versions.mix(HAPPY_HAPPY.out.versions.first()) - - happy_vcf = HAPPY_HAPPY.out.vcf - happy_tbi = HAPPY_HAPPY.out.tbi - happy_indel_roc = HAPPY_HAPPY.out.roc_indel_locations_csv - happy_indel_roc_pass = HAPPY_HAPPY.out.roc_indel_locations_pass_csv - happy_snp_roc = HAPPY_HAPPY.out.roc_snp_locations_csv - happy_snp_roc_pass = HAPPY_HAPPY.out.roc_snp_locations_pass_csv - happy_roc = HAPPY_HAPPY.out.roc_all_csv - happy_summary = HAPPY_HAPPY.out.summary_csv - happy_extended_csv = HAPPY_HAPPY.out.extended_csv - } - - if("vcfeval" in val_list_tools){ - RTGTOOLS_VCFEVAL( - ch_input, - ch_vcfeval_sdf ) - ch_versions = ch_versions.mix(RTGTOOLS_VCFEVAL.out.versions.first()) - - ch_rocplot_input = RTGTOOLS_VCFEVAL.out.snp_roc - .map { meta, tsv -> - [ meta + [roc_type:'snp'], tsv ] - } - .mix( - RTGTOOLS_VCFEVAL.out.non_snp_roc.map { meta, tsv -> - [ meta + [roc_type:'non_snp'], tsv ] - }, - RTGTOOLS_VCFEVAL.out.weighted_roc.map { meta, tsv -> - [ meta + [roc_type:'weighted'], tsv ] - } - ) - - vcfeval_true_positive_vcf = RTGTOOLS_VCFEVAL.out.tp_vcf - vcfeval_true_positive_vcf_tbi = RTGTOOLS_VCFEVAL.out.tp_tbi - vcfeval_false_negative_vcf = RTGTOOLS_VCFEVAL.out.fn_vcf - vcfeval_false_negative_vcf_tbi = RTGTOOLS_VCFEVAL.out.fn_tbi - vcfeval_false_positive_vcf = RTGTOOLS_VCFEVAL.out.fp_vcf - vcfeval_false_positive_vcf_tbi = RTGTOOLS_VCFEVAL.out.fp_tbi - vcfeval_true_positive_baseline_vcf = RTGTOOLS_VCFEVAL.out.baseline_vcf - vcfeval_true_positive_baseline_vcf_tbi = RTGTOOLS_VCFEVAL.out.baseline_tbi - vcfeval_summary = RTGTOOLS_VCFEVAL.out.summary - vcfeval_phasing = RTGTOOLS_VCFEVAL.out.phasing - vcfeval_snp_roc = RTGTOOLS_VCFEVAL.out.snp_roc - vcfeval_non_snp_roc = RTGTOOLS_VCFEVAL.out.non_snp_roc - vcfeval_weighted_roc = RTGTOOLS_VCFEVAL.out.weighted_roc - - RTGTOOLS_ROCPLOT( - ch_rocplot_input - ) - - ch_versions = ch_versions.mix(RTGTOOLS_ROCPLOT.out.versions.first()) - - rocplot_out_png = RTGTOOLS_ROCPLOT.out.png - .branch { meta, png -> - roc_type = meta.roc_type - def new_meta = meta - meta.subMap("roc_type") - snp: roc_type == "snp" - non_snp: roc_type == "non_snp" - weighted: roc_type == "weighted" - } - - rocplot_out_svg = RTGTOOLS_ROCPLOT.out.svg - .branch { meta, svg -> - roc_type = meta.roc_type - def new_meta = meta - meta.subMap("roc_type") - - snp: roc_type == "snp" - non_snp: roc_type == "non_snp" - weighted: roc_type == "weighted" - } - - rtgtools_snp_png_rocplot = rocplot_out_png.snp - rtgtools_non_snp_png_rocplot = rocplot_out_png.non_snp - rtgtools_weighted_png_rocplot = rocplot_out_png.weighted - - rtgtools_snp_svg_rocplot = rocplot_out_svg.snp - rtgtools_non_snp_svg_rocplot = rocplot_out_svg.non_snp - rtgtools_weighted_svg_rocplot = rocplot_out_svg.weighted - } + vcfeval_true_positive_vcf = RTGTOOLS_VCFEVAL.out.tp_vcf + vcfeval_true_positive_vcf_tbi = RTGTOOLS_VCFEVAL.out.tp_tbi + vcfeval_false_negative_vcf = RTGTOOLS_VCFEVAL.out.fn_vcf + vcfeval_false_negative_vcf_tbi = RTGTOOLS_VCFEVAL.out.fn_tbi + vcfeval_false_positive_vcf = RTGTOOLS_VCFEVAL.out.fp_vcf + vcfeval_false_positive_vcf_tbi = RTGTOOLS_VCFEVAL.out.fp_tbi + vcfeval_true_positive_baseline_vcf = RTGTOOLS_VCFEVAL.out.baseline_vcf + vcfeval_true_positive_baseline_vcf_tbi = RTGTOOLS_VCFEVAL.out.baseline_tbi + vcfeval_summary = RTGTOOLS_VCFEVAL.out.summary + vcfeval_phasing = RTGTOOLS_VCFEVAL.out.phasing + vcfeval_snp_roc = RTGTOOLS_VCFEVAL.out.snp_roc + vcfeval_non_snp_roc = RTGTOOLS_VCFEVAL.out.non_snp_roc + vcfeval_weighted_roc = RTGTOOLS_VCFEVAL.out.weighted_roc + + RTGTOOLS_ROCPLOT( + ch_rocplot_input + ) + + ch_versions = ch_versions.mix(RTGTOOLS_ROCPLOT.out.versions.first()) + + rocplot_out_png = RTGTOOLS_ROCPLOT.out.png + .branch { meta, png -> + roc_type = meta.roc_type + def new_meta = meta - meta.subMap("roc_type") + + snp: roc_type == "snp" + non_snp: roc_type == "non_snp" + weighted: roc_type == "weighted" + } + + rocplot_out_svg = RTGTOOLS_ROCPLOT.out.svg + .branch { meta, svg -> + roc_type = meta.roc_type + def new_meta = meta - meta.subMap("roc_type") + + snp: roc_type == "snp" + non_snp: roc_type == "non_snp" + weighted: roc_type == "weighted" + } + + rtgtools_snp_png_rocplot = rocplot_out_png.snp + rtgtools_non_snp_png_rocplot = rocplot_out_png.non_snp + rtgtools_weighted_png_rocplot = rocplot_out_png.weighted + + rtgtools_snp_svg_rocplot = rocplot_out_svg.snp + rtgtools_non_snp_svg_rocplot = rocplot_out_svg.non_snp + rtgtools_weighted_svg_rocplot = rocplot_out_svg.weighted emit: - happy_vcf // channel: [ meta, vcf ] - happy_tbi // channel: [ meta, tbi ] - happy_indel_roc // channel: [ meta, csv ] - happy_indel_roc_pass // channel: [ meta, csv ] - happy_snp_roc // channel: [ meta, csv ] - happy_snp_roc_pass // channel: [ meta, csv ] - happy_roc // channel: [ meta, csv ] - happy_summary // channel: [ meta, csv ] - happy_extended_csv // channel: [ meta, csv ] - vcfeval_true_positive_vcf // channel: [ meta, vcf ] vcfeval_true_positive_vcf_tbi // channel: [ meta, tbi ] vcfeval_false_negative_vcf // channel: [ meta, vcf ] diff --git a/workflows/germline.nf b/workflows/germline.nf index 7b51d93a..28be6851 100644 --- a/workflows/germline.nf +++ b/workflows/germline.nf @@ -672,11 +672,7 @@ workflow GERMLINE { ch_validation_input.bed, ch_fasta_ready, ch_fai_ready, - ch_sdf_ready.collect(), - [[],[]], - [[],[]], - [[],[]], - "vcfeval" //Only VCFeval for now, awaiting the conda fix for happy (https://github.com/bioconda/bioconda-recipes/pull/39267) + ch_sdf_ready.collect() ) ch_versions = ch_versions.mix(VCF_VALIDATE_SMALL_VARIANTS.out.versions) } From e94291f70d41a94f7435724619bd3fac26b7be69 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 4 Sep 2024 17:00:41 +0200 Subject: [PATCH 14/49] update all modules --- modules.json | 50 +- .../bcftools/annotate/bcftools-annotate.diff | 26 + .../nf-core/bcftools/annotate/environment.yml | 2 +- modules/nf-core/bcftools/annotate/main.nf | 20 +- modules/nf-core/bcftools/annotate/meta.yml | 16 +- .../bcftools/annotate/tests/bcf.config | 4 + .../bcftools/annotate/tests/main.nf.test | 327 ++++++++ .../bcftools/annotate/tests/main.nf.test.snap | 388 +++++++++ .../nf-core/bcftools/annotate/tests/tags.yml | 2 + .../bcftools/annotate/tests/vcf.config | 4 + .../annotate/tests/vcf_gz_index.config | 4 + .../annotate/tests/vcf_gz_index_csi.config | 4 + .../annotate/tests/vcf_gz_index_tbi.config | 4 + .../nf-core/bcftools/filter/environment.yml | 2 +- modules/nf-core/bcftools/filter/main.nf | 18 +- modules/nf-core/bcftools/filter/meta.yml | 8 + .../bcftools/filter/tests/main.nf.test | 177 +++- .../bcftools/filter/tests/main.nf.test.snap | 318 +++++++- .../bcftools/filter/tests/vcf_gz_index.config | 4 + .../filter/tests/vcf_gz_index_csi.config | 4 + .../filter/tests/vcf_gz_index_tbi.config | 4 + modules/nf-core/bcftools/norm/environment.yml | 2 +- modules/nf-core/bcftools/norm/main.nf | 22 +- modules/nf-core/bcftools/norm/meta.yml | 8 + .../nf-core/bcftools/norm/tests/main.nf.test | 563 +++++++++++++ .../bcftools/norm/tests/main.nf.test.snap | 758 ++++++++++++++++++ .../bcftools/norm/tests/nextflow.bcf.config | 4 + .../norm/tests/nextflow.bcf_gz.config | 4 + .../bcftools/norm/tests/nextflow.config | 4 + .../bcftools/norm/tests/nextflow.vcf.config | 4 + .../norm/tests/nextflow.vcf_gz.config | 4 + modules/nf-core/bcftools/norm/tests/tags.yml | 2 + .../bcftools/norm/tests/vcf_gz_index.config | 4 + .../norm/tests/vcf_gz_index_csi.config | 4 + .../norm/tests/vcf_gz_index_tbi.config | 4 + .../nf-core/bcftools/query/environment.yml | 2 +- modules/nf-core/bcftools/query/main.nf | 4 +- .../nf-core/bcftools/query/tests/main.nf.test | 16 +- .../bcftools/query/tests/main.nf.test.snap | 24 +- .../bcftools/reheader/bcftools-reheader.diff | 19 - .../nf-core/bcftools/reheader/environment.yml | 2 +- modules/nf-core/bcftools/reheader/main.nf | 15 +- modules/nf-core/bcftools/reheader/meta.yml | 4 + .../bcftools/reheader/tests/main.nf.test | 233 +++++- .../bcftools/reheader/tests/main.nf.test.snap | 345 +++++++- .../reheader/tests/vcf_gz_index.config | 4 + .../reheader/tests/vcf_gz_index_csi.config | 4 + .../reheader/tests/vcf_gz_index_tbi.config | 5 + .../nf-core/bcftools/stats/environment.yml | 3 +- modules/nf-core/bcftools/stats/main.nf | 4 +- .../nf-core/bcftools/stats/tests/main.nf.test | 182 +++++ .../bcftools/stats/tests/main.nf.test.snap | 180 +++++ modules/nf-core/bcftools/stats/tests/tags.yml | 2 + .../download/ensemblvep-download.diff | 25 - .../ensemblvep/download/environment.yml | 2 +- modules/nf-core/ensemblvep/download/main.nf | 14 +- .../ensemblvep/download/tests/main.nf.test | 60 ++ .../download/tests/main.nf.test.snap | 322 ++++++++ .../ensemblvep/download/tests/nextflow.config | 12 + .../ensemblvep/download/tests/tags.yml | 2 + modules/nf-core/gatk4/genotypegvcfs/main.nf | 18 +- .../gatk4-haplotypecaller.diff | 16 - modules/nf-core/gatk4/haplotypecaller/main.nf | 4 +- .../gatk4/haplotypecaller/tests/main.nf.test | 86 +- .../haplotypecaller/tests/main.nf.test.snap | 88 +- modules/nf-core/gawk/environment.yml | 2 +- modules/nf-core/gawk/main.nf | 9 +- modules/nf-core/gawk/tests/main.nf.test | 56 ++ modules/nf-core/gawk/tests/main.nf.test.snap | 68 ++ modules/nf-core/gawk/tests/nextflow.config | 6 + .../tests/nextflow_with_program_file.config | 5 + modules/nf-core/gawk/tests/tags.yml | 2 + modules/nf-core/mosdepth/environment.yml | 2 +- modules/nf-core/mosdepth/main.nf | 12 +- modules/nf-core/mosdepth/tests/main.nf.test | 66 +- .../nf-core/mosdepth/tests/main.nf.test.snap | 423 +++++++--- modules/nf-core/rtgtools/pedfilter/main.nf | 11 +- modules/nf-core/rtgtools/pedfilter/meta.yml | 2 +- .../pedfilter/rtgtools-pedfilter.diff | 39 - .../rtgtools/pedfilter/tests/main.nf.test | 85 ++ .../pedfilter/tests/main.nf.test.snap | 91 +++ .../rtgtools/pedfilter/tests/nextflow.config | 5 + modules/nf-core/rtgtools/rocplot/meta.yml | 2 +- .../rtgtools/rocplot/tests/main.nf.test | 16 +- .../rtgtools/rocplot/tests/main.nf.test.snap | 6 +- .../nf-core/samtools/convert/environment.yml | 4 +- modules/nf-core/samtools/convert/main.nf | 26 +- modules/nf-core/samtools/convert/meta.yml | 19 +- .../samtools/convert/tests/main.nf.test | 44 +- .../samtools/convert/tests/main.nf.test.snap | 119 ++- .../nf-core/samtools/faidx/environment.yml | 6 +- modules/nf-core/samtools/faidx/main.nf | 4 +- modules/nf-core/samtools/faidx/meta.yml | 4 + .../nf-core/samtools/faidx/tests/main.nf.test | 122 +++ .../samtools/faidx/tests/main.nf.test.snap | 249 ++++++ .../samtools/faidx/tests/nextflow.config | 7 + .../samtools/faidx/tests/nextflow2.config | 6 + modules/nf-core/samtools/faidx/tests/tags.yml | 2 + .../nf-core/samtools/index/environment.yml | 4 +- modules/nf-core/samtools/index/main.nf | 11 +- .../nf-core/samtools/index/tests/main.nf.test | 87 +- .../samtools/index/tests/main.nf.test.snap | 264 +++++- .../nf-core/samtools/merge/environment.yml | 4 +- modules/nf-core/samtools/merge/main.nf | 4 +- .../samtools/merge/samtools-merge.diff | 13 - .../samtools/merge/tests/main.nf.test.snap | 24 +- .../nf-core/somalier/extract/environment.yml | 2 +- modules/nf-core/somalier/extract/main.nf | 10 +- modules/nf-core/somalier/extract/meta.yml | 17 +- .../somalier/extract/tests/main.nf.test | 84 ++ .../somalier/extract/tests/main.nf.test.snap | 72 ++ .../nf-core/somalier/extract/tests/tags.yml | 2 + .../nf-core/somalier/relate/environment.yml | 7 - modules/nf-core/somalier/relate/main.nf | 62 -- modules/nf-core/somalier/relate/meta.yml | 63 -- .../somalier/relate/somalier-relate.diff | 30 - modules/nf-core/tabix/bgzip/environment.yml | 1 + modules/nf-core/tabix/bgzip/main.nf | 7 +- .../tabix/bgzip/tests/bgzip_compress.config | 5 + .../nf-core/tabix/bgzip/tests/main.nf.test | 111 +++ .../tabix/bgzip/tests/main.nf.test.snap | 218 +++++ modules/nf-core/tabix/bgzip/tests/tags.yml | 2 + .../nf-core/tabix/bgzip/tests/vcf_none.config | 5 + .../nf-core/tabix/bgziptabix/environment.yml | 1 + modules/nf-core/tabix/bgziptabix/main.nf | 8 +- .../tabix/bgziptabix/tests/main.nf.test | 94 +++ .../tabix/bgziptabix/tests/main.nf.test.snap | 167 ++++ .../tabix/bgziptabix/tests/tabix_csi.config | 5 + .../tabix/bgziptabix/tests/tabix_tbi.config | 5 + .../nf-core/tabix/bgziptabix/tests/tags.yml | 2 + modules/nf-core/untar/environment.yml | 4 +- modules/nf-core/untar/main.nf | 29 +- modules/nf-core/untar/tests/main.nf.test | 44 +- modules/nf-core/untar/tests/main.nf.test.snap | 152 +++- modules/nf-core/vardictjava/environment.yml | 1 + modules/nf-core/vardictjava/main.nf | 15 +- modules/nf-core/vardictjava/meta.yml | 2 +- .../nf-core/vardictjava/tests/main.nf.test | 24 +- .../vardictjava/tests/main.nf.test.snap | 20 +- modules/nf-core/vardictjava/vardictjava.diff | 13 - modules/nf-core/vcf2db/Dockerfile | 11 - modules/nf-core/vcf2db/main.nf | 10 +- modules/nf-core/vcf2db/tests/main.nf.test | 14 +- .../nf-core/vcf2db/tests/main.nf.test.snap | 40 +- modules/nf-core/vcf2db/vcf2db_env.yaml | 96 --- .../local/gvcf_joint_genotype_gatk4/main.nf | 6 +- .../local/vcf_extract_relate_somalier/main.nf | 6 +- workflows/germline.nf | 18 +- 148 files changed, 6842 insertions(+), 1044 deletions(-) create mode 100644 modules/nf-core/bcftools/annotate/bcftools-annotate.diff create mode 100644 modules/nf-core/bcftools/annotate/tests/bcf.config create mode 100644 modules/nf-core/bcftools/annotate/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/annotate/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/annotate/tests/tags.yml create mode 100644 modules/nf-core/bcftools/annotate/tests/vcf.config create mode 100644 modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config create mode 100644 modules/nf-core/bcftools/filter/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/filter/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/filter/tests/vcf_gz_index_tbi.config create mode 100644 modules/nf-core/bcftools/norm/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/norm/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/norm/tests/nextflow.bcf.config create mode 100644 modules/nf-core/bcftools/norm/tests/nextflow.bcf_gz.config create mode 100644 modules/nf-core/bcftools/norm/tests/nextflow.config create mode 100644 modules/nf-core/bcftools/norm/tests/nextflow.vcf.config create mode 100644 modules/nf-core/bcftools/norm/tests/nextflow.vcf_gz.config create mode 100644 modules/nf-core/bcftools/norm/tests/tags.yml create mode 100644 modules/nf-core/bcftools/norm/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/norm/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/norm/tests/vcf_gz_index_tbi.config delete mode 100644 modules/nf-core/bcftools/reheader/bcftools-reheader.diff create mode 100644 modules/nf-core/bcftools/reheader/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/reheader/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/reheader/tests/vcf_gz_index_tbi.config create mode 100644 modules/nf-core/bcftools/stats/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/stats/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/stats/tests/tags.yml delete mode 100644 modules/nf-core/ensemblvep/download/ensemblvep-download.diff create mode 100644 modules/nf-core/ensemblvep/download/tests/main.nf.test create mode 100644 modules/nf-core/ensemblvep/download/tests/main.nf.test.snap create mode 100644 modules/nf-core/ensemblvep/download/tests/nextflow.config create mode 100644 modules/nf-core/ensemblvep/download/tests/tags.yml delete mode 100644 modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff create mode 100644 modules/nf-core/gawk/tests/main.nf.test create mode 100644 modules/nf-core/gawk/tests/main.nf.test.snap create mode 100644 modules/nf-core/gawk/tests/nextflow.config create mode 100644 modules/nf-core/gawk/tests/nextflow_with_program_file.config create mode 100644 modules/nf-core/gawk/tests/tags.yml delete mode 100644 modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff create mode 100644 modules/nf-core/rtgtools/pedfilter/tests/main.nf.test create mode 100644 modules/nf-core/rtgtools/pedfilter/tests/main.nf.test.snap create mode 100644 modules/nf-core/rtgtools/pedfilter/tests/nextflow.config create mode 100644 modules/nf-core/samtools/faidx/tests/main.nf.test create mode 100644 modules/nf-core/samtools/faidx/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/faidx/tests/nextflow.config create mode 100644 modules/nf-core/samtools/faidx/tests/nextflow2.config create mode 100644 modules/nf-core/samtools/faidx/tests/tags.yml delete mode 100644 modules/nf-core/samtools/merge/samtools-merge.diff create mode 100644 modules/nf-core/somalier/extract/tests/main.nf.test create mode 100644 modules/nf-core/somalier/extract/tests/main.nf.test.snap create mode 100644 modules/nf-core/somalier/extract/tests/tags.yml delete mode 100644 modules/nf-core/somalier/relate/environment.yml delete mode 100644 modules/nf-core/somalier/relate/main.nf delete mode 100644 modules/nf-core/somalier/relate/meta.yml delete mode 100644 modules/nf-core/somalier/relate/somalier-relate.diff create mode 100644 modules/nf-core/tabix/bgzip/tests/bgzip_compress.config create mode 100644 modules/nf-core/tabix/bgzip/tests/main.nf.test create mode 100644 modules/nf-core/tabix/bgzip/tests/main.nf.test.snap create mode 100644 modules/nf-core/tabix/bgzip/tests/tags.yml create mode 100644 modules/nf-core/tabix/bgzip/tests/vcf_none.config create mode 100644 modules/nf-core/tabix/bgziptabix/tests/main.nf.test create mode 100644 modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap create mode 100644 modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config create mode 100644 modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config create mode 100644 modules/nf-core/tabix/bgziptabix/tests/tags.yml delete mode 100644 modules/nf-core/vardictjava/vardictjava.diff delete mode 100644 modules/nf-core/vcf2db/Dockerfile delete mode 100644 modules/nf-core/vcf2db/vcf2db_env.yaml diff --git a/modules.json b/modules.json index 830e32fa..16f83c21 100644 --- a/modules.json +++ b/modules.json @@ -7,8 +7,9 @@ "nf-core": { "bcftools/annotate": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": ["modules"] + "git_sha": "88ae68490e8f2478a1e1bbeedac970fd7cc73022", + "installed_by": ["modules"], + "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff" }, "bcftools/concat": { "branch": "master", @@ -17,12 +18,12 @@ }, "bcftools/filter": { "branch": "master", - "git_sha": "a3893076a76e91b3ff152faddf872f00778fb224", + "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988", "installed_by": ["modules"] }, "bcftools/norm": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", + "git_sha": "f6cc00f107826cfaf1c933297b10ed1757b41479", "installed_by": ["modules"] }, "bcftools/pluginscatter": { @@ -32,12 +33,12 @@ }, "bcftools/query": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", + "git_sha": "34ac993e081b32d2170ab790d0386b74122f9d36", "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", + "git_sha": "c32611ac6813055b9321d2827678e2f8aebcb394", "installed_by": ["modules"] }, "bcftools/sort": { @@ -47,7 +48,7 @@ }, "bcftools/stats": { "branch": "master", - "git_sha": "618364f55cb88f6c283f6c6c45c24d5f9f08f998", + "git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f", "installed_by": ["modules"] }, "bedtools/intersect": { @@ -102,17 +103,17 @@ }, "gatk4/haplotypecaller": { "branch": "master", - "git_sha": "e53d091a6de1ae9fd681351c085d8abe076ba1ec", + "git_sha": "c332ea831f95f750be962c4b5de655f7a1e6e245", "installed_by": ["modules"] }, "gawk": { "branch": "master", - "git_sha": "da4d05d04e65227d4307e87940842f1a14de62c7", + "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", "installed_by": ["modules"] }, "mosdepth": { "branch": "master", - "git_sha": "69e3eb17fb31b772b18f134d6e8f8b93ee980e65", + "git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb", "installed_by": ["modules"] }, "multiqc": { @@ -127,12 +128,12 @@ }, "rtgtools/pedfilter": { "branch": "master", - "git_sha": "1a4ab76618a2269ee653aefff8a5ee1f855e5f83", + "git_sha": "c1c2a770cfb0bfbf093a2434a27f091ebbc65987", "installed_by": ["modules"] }, "rtgtools/rocplot": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "64770369d851c45c364e410e052ef9a6c3a7d2bb", "installed_by": ["modules"] }, "rtgtools/vcfeval": { @@ -142,22 +143,22 @@ }, "samtools/convert": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": ["modules"] }, "samtools/index": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": ["modules"] }, "snpeff/snpeff": { @@ -167,22 +168,17 @@ }, "somalier/extract": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] - }, - "somalier/relate": { - "branch": "master", - "git_sha": "d8ba32c6b54a01f8efa7b51a1f3978f003f8873b", + "git_sha": "458c882987320e27fc90723ec96c127a243a5497", "installed_by": ["modules"] }, "tabix/bgzip": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "b20be35facfc5acdc1259f132ed79339d79e989f", "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", "installed_by": ["modules"] }, "tabix/tabix": { @@ -192,17 +188,17 @@ }, "untar": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", "installed_by": ["modules"] }, "vardictjava": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "e61e5a13ef49c5595986bd31efb85c3f0709a282", "installed_by": ["modules"] }, "vcf2db": { "branch": "master", - "git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d", + "git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006", "installed_by": ["modules"] }, "vcfanno": { diff --git a/modules/nf-core/bcftools/annotate/bcftools-annotate.diff b/modules/nf-core/bcftools/annotate/bcftools-annotate.diff new file mode 100644 index 00000000..518cee56 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/bcftools-annotate.diff @@ -0,0 +1,26 @@ +Changes in module 'nf-core/bcftools/annotate' +Changes in 'bcftools/annotate/main.nf': +--- modules/nf-core/bcftools/annotate/main.nf ++++ modules/nf-core/bcftools/annotate/main.nf +@@ -8,8 +8,7 @@ + 'biocontainers/bcftools:1.20--h8b25389_0' }" + + input: +- tuple val(meta), path(input), path(index), path(annotations), path(annotations_index) +- path(header_lines) ++ tuple val(meta), path(input), path(index), path(annotations), path(annotations_index), path(header_lines) + + output: + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + +'modules/nf-core/bcftools/annotate/environment.yml' is unchanged +'modules/nf-core/bcftools/annotate/meta.yml' is unchanged +'modules/nf-core/bcftools/annotate/tests/tags.yml' is unchanged +'modules/nf-core/bcftools/annotate/tests/vcf.config' is unchanged +'modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config' is unchanged +'modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config' is unchanged +'modules/nf-core/bcftools/annotate/tests/main.nf.test' is unchanged +'modules/nf-core/bcftools/annotate/tests/bcf.config' is unchanged +'modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config' is unchanged +'modules/nf-core/bcftools/annotate/tests/main.nf.test.snap' is unchanged +************************************************************ diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml index e0abc8d2..3d4e3379 100644 --- a/modules/nf-core/bcftools/annotate/environment.yml +++ b/modules/nf-core/bcftools/annotate/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index 27ebfd4a..2cfe29a1 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -4,14 +4,16 @@ process BCFTOOLS_ANNOTATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(input), path(index), path(annotations), path(annotations_index), path(header_lines) output: tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true path "versions.yml" , emit: versions when: @@ -27,8 +29,12 @@ process BCFTOOLS_ANNOTATE { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + def index_command = !index ? "bcftools index $input" : '' + if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" """ + $index_command + bcftools \\ annotate \\ $args \\ @@ -52,8 +58,16 @@ process BCFTOOLS_ANNOTATE { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + """ - touch ${prefix}.${extension} + ${create_cmd} ${prefix}.${extension} + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/annotate/meta.yml b/modules/nf-core/bcftools/annotate/meta.yml index f3aa463b..248eee0c 100644 --- a/modules/nf-core/bcftools/annotate/meta.yml +++ b/modules/nf-core/bcftools/annotate/meta.yml @@ -40,14 +40,22 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: type: file description: Compressed annotated VCF file pattern: "*{vcf,vcf.gz,bcf,bcf.gz}" + - csi: + type: file + description: Default VCF file index + pattern: "*.csi" + - tbi: + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@projectoriented" - "@ramprasadn" diff --git a/modules/nf-core/bcftools/annotate/tests/bcf.config b/modules/nf-core/bcftools/annotate/tests/bcf.config new file mode 100644 index 00000000..79d26779 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/bcf.config @@ -0,0 +1,4 @@ +process { + ext.args = "-x ID,INFO/DP,FORMAT/DP --output-type u" + ext.prefix = { "${meta.id}_ann" } +} diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test b/modules/nf-core/bcftools/annotate/tests/main.nf.test new file mode 100644 index 00000000..3a5c4933 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test @@ -0,0 +1,327 @@ +nextflow_process { + + name "Test Process BCFTOOLS_ANNOTATE" + script "../main.nf" + process "BCFTOOLS_ANNOTATE" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/annotate" + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output") { + + config "./vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output") { + + config "./vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.versions + ).match() } + ) + } + + } + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + test("sarscov2 - [vcf, [], annotation, annotation_tbi], header - bcf_output") { + + config "./bcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = Channel.of( + '##INFO=', + '##INFO=' + ).collectFile(name:"headers.vcf", newLine:true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.versions + ).match("bcf") } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub") { + + config "./vcf.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match()}, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap new file mode 100644 index 00000000..bac2224a --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap @@ -0,0 +1,388 @@ +{ + "bcf": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_ann.bcf" + ] + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-12T16:39:33.331888" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:07:59.658031137" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:09:05.096883418" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:08:10.581301219" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:08:43.975017625" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi" + ] + ], + [ + + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:08:21.354059092" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:07:37.788393317" + }, + "sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:07:48.500746325" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:09:16.094918834" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:08:54.366358502" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/annotate/tests/tags.yml b/modules/nf-core/bcftools/annotate/tests/tags.yml new file mode 100644 index 00000000..f97a1afc --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/annotate: + - "modules/nf-core/bcftools/annotate/**" diff --git a/modules/nf-core/bcftools/annotate/tests/vcf.config b/modules/nf-core/bcftools/annotate/tests/vcf.config new file mode 100644 index 00000000..611868d5 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/vcf.config @@ -0,0 +1,4 @@ +process { + ext.args = "-x ID,INFO/DP,FORMAT/DP --output-type z" + ext.prefix = { "${meta.id}_vcf" } +} diff --git a/modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config new file mode 100644 index 00000000..2fd9a225 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.args = "--output-type z --write-index --no-version" + ext.prefix = { "${meta.id}_vcf" } +} diff --git a/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..512c1dfb --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.args = "--output-type z --write-index=csi --no-version" + ext.prefix = { "${meta.id}_vcf" } +} diff --git a/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..7feb5ebb --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.args = "--output-type z --write-index=tbi --no-version" + ext.prefix = { "${meta.id}_vcf" } +} diff --git a/modules/nf-core/bcftools/filter/environment.yml b/modules/nf-core/bcftools/filter/environment.yml index b2698757..854de139 100644 --- a/modules/nf-core/bcftools/filter/environment.yml +++ b/modules/nf-core/bcftools/filter/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf index cc9a2361..8f92c51a 100644 --- a/modules/nf-core/bcftools/filter/main.nf +++ b/modules/nf-core/bcftools/filter/main.nf @@ -4,14 +4,16 @@ process BCFTOOLS_FILTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcf) output: tuple val(meta), path("*.${extension}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true path "versions.yml" , emit: versions when: @@ -45,19 +47,23 @@ process BCFTOOLS_FILTER { stub: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" - def create_file = extension.endsWith(".gz") ? "echo '' | gzip > ${prefix}.${extension}" : "touch ${prefix}.${extension}" - """ - ${create_file} + ${create_cmd} ${prefix}.${extension} + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/filter/meta.yml b/modules/nf-core/bcftools/filter/meta.yml index deb93b13..d67c0257 100644 --- a/modules/nf-core/bcftools/filter/meta.yml +++ b/modules/nf-core/bcftools/filter/meta.yml @@ -32,6 +32,14 @@ output: type: file description: VCF filtered output file pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - csi: + type: file + description: Default VCF file index + pattern: "*.csi" + - tbi: + type: file + description: Alternative VCF file index + pattern: "*.tbi" - versions: type: file description: File containing software versions diff --git a/modules/nf-core/bcftools/filter/tests/main.nf.test b/modules/nf-core/bcftools/filter/tests/main.nf.test index eaf100e8..646f37ad 100644 --- a/modules/nf-core/bcftools/filter/tests/main.nf.test +++ b/modules/nf-core/bcftools/filter/tests/main.nf.test @@ -9,10 +9,10 @@ nextflow_process { tag "bcftools" tag "bcftools/filter" - config "./nextflow.config" - test("sarscov2 - vcf") { + config "./nextflow.config" + when { process { """ @@ -33,8 +33,100 @@ nextflow_process { } + test("sarscov2 - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + test("sarscov2 - vcf - bcf output") { + config "./nextflow.config" + when { process { """ @@ -57,6 +149,7 @@ nextflow_process { test("sarscov2 - vcf - stub") { + config "./nextflow.config" options "-stub" when { @@ -79,4 +172,82 @@ nextflow_process { } -} + test("sarscov2 - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/filter/tests/main.nf.test.snap b/modules/nf-core/bcftools/filter/tests/main.nf.test.snap index f8e17aa0..3d7605f2 100644 --- a/modules/nf-core/bcftools/filter/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/filter/tests/main.nf.test.snap @@ -1,4 +1,59 @@ { + "sarscov2 - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T13:59:08.235854993" + }, "vcf": { "content": [ { @@ -11,7 +66,19 @@ ] ], "1": [ - "versions.yml:md5,7dc77043f9afb848d942d47a7bc19f67" + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ], + "csi": [ + + ], + "tbi": [ + ], "vcf": [ [ @@ -22,15 +89,15 @@ ] ], "versions": [ - "versions.yml:md5,7dc77043f9afb848d942d47a7bc19f67" + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-27T16:57:32.940161987" + "timestamp": "2024-06-04T15:20:28.427974818" }, "bcf output": { "content": [ @@ -44,7 +111,19 @@ ] ], "1": [ - "versions.yml:md5,7dc77043f9afb848d942d47a7bc19f67" + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ], + "csi": [ + + ], + "tbi": [ + ], "vcf": [ [ @@ -55,15 +134,77 @@ ] ], "versions": [ - "versions.yml:md5,7dc77043f9afb848d942d47a7bc19f67" + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T15:20:34.049236749" + }, + "sarscov2 - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" }, - "timestamp": "2024-03-27T16:45:14.586866398" + "timestamp": "2024-06-05T08:09:49.837854646" + }, + "sarscov2 - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T13:57:19.513365022" }, "vcf - stub": { "content": [ @@ -77,7 +218,19 @@ ] ], "1": [ - "versions.yml:md5,7dc77043f9afb848d942d47a7bc19f67" + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ], + "csi": [ + + ], + "tbi": [ + ], "vcf": [ [ @@ -88,14 +241,155 @@ ] ], "versions": [ - "versions.yml:md5,7dc77043f9afb848d942d47a7bc19f67" + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T15:29:55.846566153" + }, + "sarscov2 - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ], + "csi": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T15:59:37.636874258" + }, + "sarscov2 - vcf_gz_index_csi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ], + "csi": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T13:58:46.36278584" + }, + "sarscov2 - vcf_gz_index_tbi": { + "content": [ + [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + + ], + [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" }, - "timestamp": "2024-03-27T17:05:52.80837892" + "timestamp": "2024-06-05T13:57:34.748836577" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/filter/tests/vcf_gz_index.config b/modules/nf-core/bcftools/filter/tests/vcf_gz_index.config new file mode 100644 index 00000000..7dd696ee --- /dev/null +++ b/modules/nf-core/bcftools/filter/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index --no-version" +} diff --git a/modules/nf-core/bcftools/filter/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/filter/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..aebffb6f --- /dev/null +++ b/modules/nf-core/bcftools/filter/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi --no-version" +} diff --git a/modules/nf-core/bcftools/filter/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/filter/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..b192ae7d --- /dev/null +++ b/modules/nf-core/bcftools/filter/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi --no-version" +} diff --git a/modules/nf-core/bcftools/norm/environment.yml b/modules/nf-core/bcftools/norm/environment.yml index fe80e4e7..0c7dfa8f 100644 --- a/modules/nf-core/bcftools/norm/environment.yml +++ b/modules/nf-core/bcftools/norm/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index 47d3dab1..bd7a2501 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -4,16 +4,18 @@ process BCFTOOLS_NORM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcf), path(tbi) tuple val(meta2), path(fasta) output: - tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}") , emit: vcf - path "versions.yml" , emit: versions + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -30,7 +32,7 @@ process BCFTOOLS_NORM { """ bcftools norm \\ --fasta-ref ${fasta} \\ - --output ${prefix}.${extension}\\ + --output ${prefix}.${extension} \\ $args \\ --threads $task.cpus \\ ${vcf} @@ -49,8 +51,16 @@ process BCFTOOLS_NORM { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf.gz" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + """ - touch ${prefix}.${extension} + ${create_cmd} ${prefix}.${extension} + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/norm/meta.yml b/modules/nf-core/bcftools/norm/meta.yml index 1f3e1b62..a0cdeaf1 100644 --- a/modules/nf-core/bcftools/norm/meta.yml +++ b/modules/nf-core/bcftools/norm/meta.yml @@ -49,6 +49,14 @@ output: type: file description: One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - csi: + type: file + description: Default VCF file index + pattern: "*.csi" + - tbi: + type: file + description: Alternative VCF file index + pattern: "*.tbi" - versions: type: file description: File containing software versions diff --git a/modules/nf-core/bcftools/norm/tests/main.nf.test b/modules/nf-core/bcftools/norm/tests/main.nf.test new file mode 100644 index 00000000..dbc41502 --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/main.nf.test @@ -0,0 +1,563 @@ +nextflow_process { + + name "Test Process BCFTOOLS_NORM" + script "../main.nf" + process "BCFTOOLS_NORM" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/norm" + + test("sarscov2 - [ vcf, [] ], fasta") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } } + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } } + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } } + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta - vcf output") { + + config "./nextflow.vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta - vcf_gz output") { + + config "./nextflow.vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta - bcf output") { + + config "./nextflow.bcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta - bcf_gz output") { + + config "./nextflow.bcf_gz.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, [] ], fasta - stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta -stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta - vcf output -stub") { + + config "./nextflow.vcf.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta - vcf_gz output - stub") { + + config "./nextflow.vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta - bcf output - stub") { + + config "./nextflow.bcf.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta - bcf_gz output - stub") { + + config "./nextflow.bcf_gz.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/norm/tests/main.nf.test.snap b/modules/nf-core/bcftools/norm/tests/main.nf.test.snap new file mode 100644 index 00000000..3be52116 --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/main.nf.test.snap @@ -0,0 +1,758 @@ +{ + "sarscov2 - 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[ vcf, [] ], fasta - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,63e5adbaf3dd94550e9e3d7935dd28db" + ] + ], + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T13:53:09.808834237" + }, + "sarscov2 - [ vcf, tbi ], fasta - bcf output": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_norm.bcf.gz:md5,638c3c25bdd495c90ecbccb69ee77f07" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,ff760495922469e56d0fc3372773000d" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_norm.bcf.gz:md5,638c3c25bdd495c90ecbccb69ee77f07" + ] + ], + "versions": [ + "versions.yml:md5,ff760495922469e56d0fc3372773000d" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T14:37:42.141945244" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/norm/tests/nextflow.bcf.config b/modules/nf-core/bcftools/norm/tests/nextflow.bcf.config new file mode 100644 index 00000000..b79af868 --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/nextflow.bcf.config @@ -0,0 +1,4 @@ +process { + ext.args = '-m -any --output-type b --no-version' + ext.prefix = "test_norm" +} diff --git a/modules/nf-core/bcftools/norm/tests/nextflow.bcf_gz.config b/modules/nf-core/bcftools/norm/tests/nextflow.bcf_gz.config new file mode 100644 index 00000000..f36f397c --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/nextflow.bcf_gz.config @@ -0,0 +1,4 @@ +process { + ext.args = '-m -any --output-type u --no-version' + ext.prefix = "test_norm" +} diff --git a/modules/nf-core/bcftools/norm/tests/nextflow.config b/modules/nf-core/bcftools/norm/tests/nextflow.config new file mode 100644 index 00000000..510803b4 --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/nextflow.config @@ -0,0 +1,4 @@ +process { + ext.args = '-m -any --no-version' + ext.prefix = "test_norm" +} diff --git a/modules/nf-core/bcftools/norm/tests/nextflow.vcf.config b/modules/nf-core/bcftools/norm/tests/nextflow.vcf.config new file mode 100644 index 00000000..10bf93e3 --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/nextflow.vcf.config @@ -0,0 +1,4 @@ +process { + ext.args = '-m -any --output-type v --no-version' + ext.prefix = "test_norm" +} diff --git a/modules/nf-core/bcftools/norm/tests/nextflow.vcf_gz.config b/modules/nf-core/bcftools/norm/tests/nextflow.vcf_gz.config new file mode 100644 index 00000000..b31dd2de --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/nextflow.vcf_gz.config @@ -0,0 +1,4 @@ +process { + ext.args = '-m -any --output-type z ---no-version' + ext.prefix = "test_norm" +} diff --git a/modules/nf-core/bcftools/norm/tests/tags.yml b/modules/nf-core/bcftools/norm/tests/tags.yml new file mode 100644 index 00000000..f6f5e356 --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/norm: + - "modules/nf-core/bcftools/norm/**" diff --git a/modules/nf-core/bcftools/norm/tests/vcf_gz_index.config b/modules/nf-core/bcftools/norm/tests/vcf_gz_index.config new file mode 100644 index 00000000..7dd696ee --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index --no-version" +} diff --git a/modules/nf-core/bcftools/norm/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/norm/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..aebffb6f --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi --no-version" +} diff --git a/modules/nf-core/bcftools/norm/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/norm/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..b192ae7d --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi --no-version" +} diff --git a/modules/nf-core/bcftools/query/environment.yml b/modules/nf-core/bcftools/query/environment.yml index 4f9661ca..d8c4f4e4 100644 --- a/modules/nf-core/bcftools/query/environment.yml +++ b/modules/nf-core/bcftools/query/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf index e9e73a6a..58019f4d 100644 --- a/modules/nf-core/bcftools/query/main.nf +++ b/modules/nf-core/bcftools/query/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_QUERY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/query/tests/main.nf.test b/modules/nf-core/bcftools/query/tests/main.nf.test index e9ea5a9d..39e67b35 100644 --- a/modules/nf-core/bcftools/query/tests/main.nf.test +++ b/modules/nf-core/bcftools/query/tests/main.nf.test @@ -18,8 +18,8 @@ nextflow_process { """ input[0] = [ [ id:'out' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) ] input[1] = [] input[2] = [] @@ -47,11 +47,11 @@ nextflow_process { """ input[0] = [ [ id:'out' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) ] - input[1] = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz', checkIfExists: true) input[3] = [] """ } @@ -76,8 +76,8 @@ nextflow_process { """ input[0] = [ [ id:'out' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) ] input[1] = [] input[2] = [] diff --git a/modules/nf-core/bcftools/query/tests/main.nf.test.snap b/modules/nf-core/bcftools/query/tests/main.nf.test.snap index a19f2053..3ead1f2c 100644 --- a/modules/nf-core/bcftools/query/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/query/tests/main.nf.test.snap @@ -10,19 +10,27 @@ ] ], [ - "versions.yml:md5,b40206d5437ce4b044d15c47ddd93d8e" + "versions.yml:md5,3d93ea9cd5d314743254618b49e4bd16" ] ], - "timestamp": "2023-11-29T14:21:05.191946862" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T15:15:44.916249758" }, "sarscov2 - [vcf, tbi], [], [], [] - stub": { "content": [ "out.txt", [ - "versions.yml:md5,b40206d5437ce4b044d15c47ddd93d8e" + "versions.yml:md5,3d93ea9cd5d314743254618b49e4bd16" ] ], - "timestamp": "2023-11-29T14:21:11.169603542" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T15:15:49.932359271" }, "sarscov2 - [vcf, tbi], [], [], []": { "content": [ @@ -35,9 +43,13 @@ ] ], [ - "versions.yml:md5,b40206d5437ce4b044d15c47ddd93d8e" + "versions.yml:md5,3d93ea9cd5d314743254618b49e4bd16" ] ], - "timestamp": "2023-11-29T14:20:59.335041418" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T15:15:39.930697926" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/reheader/bcftools-reheader.diff b/modules/nf-core/bcftools/reheader/bcftools-reheader.diff deleted file mode 100644 index 57637baa..00000000 --- a/modules/nf-core/bcftools/reheader/bcftools-reheader.diff +++ /dev/null @@ -1,19 +0,0 @@ -Changes in module 'nf-core/bcftools/reheader' ---- modules/nf-core/bcftools/reheader/main.nf -+++ modules/nf-core/bcftools/reheader/main.nf -@@ -31,10 +31,13 @@ - args2.contains("--output-type v") || args2.contains("-Ov") ? "vcf" : - "vcf" - """ -+ echo ${meta.sample} > sample.txt -+ - bcftools \\ - reheader \\ - $update_sequences \\ - $new_header \\ -+ --samples sample.txt \\ - $args \\ - --threads $task.cpus \\ - $vcf \\ - -************************************************************ diff --git a/modules/nf-core/bcftools/reheader/environment.yml b/modules/nf-core/bcftools/reheader/environment.yml index aab0dc92..48fd72c9 100644 --- a/modules/nf-core/bcftools/reheader/environment.yml +++ b/modules/nf-core/bcftools/reheader/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/reheader/main.nf b/modules/nf-core/bcftools/reheader/main.nf index 82527167..9cf6d0d3 100644 --- a/modules/nf-core/bcftools/reheader/main.nf +++ b/modules/nf-core/bcftools/reheader/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_REHEADER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcf), path(header), path(samples) @@ -13,6 +13,7 @@ process BCFTOOLS_REHEADER { output: tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.{csi,tbi}") , emit: index, optional: true path "versions.yml" , emit: versions when: @@ -59,8 +60,16 @@ process BCFTOOLS_REHEADER { args2.contains("--output-type z") || args2.contains("-Oz") ? "vcf.gz" : args2.contains("--output-type v") || args2.contains("-Ov") ? "vcf" : "vcf" + def index = args2.contains("--write-index=tbi") || args2.contains("-W=tbi") ? "tbi" : + args2.contains("--write-index=csi") || args2.contains("-W=csi") ? "csi" : + args2.contains("--write-index") || args2.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + """ - touch ${prefix}.${extension} + ${create_cmd} ${prefix}.${extension} + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/reheader/meta.yml b/modules/nf-core/bcftools/reheader/meta.yml index 690d4ead..d903cc0f 100644 --- a/modules/nf-core/bcftools/reheader/meta.yml +++ b/modules/nf-core/bcftools/reheader/meta.yml @@ -53,6 +53,10 @@ output: type: file description: VCF with updated header, bgzipped per default pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - index: + type: file + description: Index of VCF with updated header + pattern: "*.{csi,tbi}" authors: - "@bjohnnyd" - "@jemten" diff --git a/modules/nf-core/bcftools/reheader/tests/main.nf.test b/modules/nf-core/bcftools/reheader/tests/main.nf.test index f3200cb3..96c1b7b0 100644 --- a/modules/nf-core/bcftools/reheader/tests/main.nf.test +++ b/modules/nf-core/bcftools/reheader/tests/main.nf.test @@ -17,13 +17,13 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [], [] ] - input[1] = [ + input[1] = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] """ } @@ -47,13 +47,13 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [], [] ] - input[1] = [ + input[1] = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] """ } @@ -68,6 +68,111 @@ nextflow_process { } + test("sarscov2 - [vcf, [], []], fai - vcf.gz output - index") { + + config "./vcf_gz_index.config" + when { + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.index[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index") { + + config "./vcf_gz_index_csi.config" + when { + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.index[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index") { + + config "./vcf_gz_index_tbi.config" + when { + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.index[0][1].endsWith(".tbi") } + ) + } + + } + test("sarscov2 - [vcf, [], []], fai - bcf output") { config "./bcf.config" @@ -77,13 +182,13 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [], [] ] - input[1] = [ + input[1] = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] """ } @@ -107,11 +212,11 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), [] ] - input[1] = [ + input[1] = [ [ id:'genome' ], // meta map [] ] @@ -137,15 +242,15 @@ nextflow_process { """ ch_no_samples = Channel.of([ [ id:'test', single_end:false ], - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [] ]) ch_samples = Channel.of(["samples.txt", "new_name"]) .collectFile(newLine:true) input[0] = ch_no_samples.combine(ch_samples) - input[1] = [ + input[1] = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] """ } @@ -170,13 +275,13 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [], [] ] - input[1] = [ + input[1] = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] """ } @@ -193,5 +298,97 @@ nextflow_process { } } + test("sarscov2 - [vcf, [], []], fai - vcf.gz output - index -stub") { + + options "-stub" + config "./vcf_gz_index.config" + when { + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index -stub") { + + options "-stub" + config "./vcf_gz_index_csi.config" + when { + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index -stub") { + + options "-stub" + config "./vcf_gz_index_tbi.config" + when { + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } } diff --git a/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap b/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap index 112736a1..87a3654a 100644 --- a/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap @@ -1,4 +1,140 @@ { + "sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T10:09:05.955833763" + }, + "sarscov2 - [vcf, [], []], fai - vcf.gz output - index -stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ], + "index": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T09:52:41.444952182" + }, + "sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index -stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ], + "index": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T09:53:04.314827944" + }, "sarscov2 - [vcf, [], []], fai - vcf output": { "content": [ { @@ -12,7 +148,13 @@ ] ], "1": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + + ], + "2": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ], + "index": [ + ], "vcf": [ [ @@ -24,11 +166,15 @@ ] ], "versions": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" ] } ], - "timestamp": "2023-11-29T13:05:44.058376693" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T09:50:41.983008108" }, "sarscov2 - [vcf, [], []], fai - bcf output": { "content": [ @@ -39,11 +185,17 @@ "id": "test", "single_end": false }, - "tested.bcf.gz:md5,c31d9afd8614832c2a46d9a55682c97a" + "tested.bcf.gz:md5,c8a304c8d2892039201154153c8cd536" ] ], "1": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + + ], + "2": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ], + "index": [ + ], "vcf": [ [ @@ -51,15 +203,19 @@ "id": "test", "single_end": false }, - "tested.bcf.gz:md5,c31d9afd8614832c2a46d9a55682c97a" + "tested.bcf.gz:md5,c8a304c8d2892039201154153c8cd536" ] ], "versions": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" ] } ], - "timestamp": "2023-11-29T13:06:03.793372514" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T09:51:43.072513252" }, "sarscov2 - [vcf, [], []], fai - vcf.gz output": { "content": [ @@ -70,11 +226,17 @@ "id": "test", "single_end": false }, - "tested.vcf.gz:md5,a1e45fe6d2b386fc2611766e5d2937ee" + "tested.vcf.gz:md5,8e722884ffb75155212a3fc053918766" ] ], "1": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + + ], + "2": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ], + "index": [ + ], "vcf": [ [ @@ -82,24 +244,145 @@ "id": "test", "single_end": false }, - "tested.vcf.gz:md5,a1e45fe6d2b386fc2611766e5d2937ee" + "tested.vcf.gz:md5,8e722884ffb75155212a3fc053918766" ] ], "versions": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" ] } ], - "timestamp": "2023-11-29T13:05:53.954090441" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T09:50:53.055630152" + }, + "sarscov2 - [vcf, [], []], fai - vcf.gz output - index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T10:08:37.999924355" + }, + "sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index -stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ], + "index": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T09:52:52.512269206" }, "sarscov2 - [vcf, [], []], fai - stub": { "content": [ "tested.vcf", [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" ] ], - "timestamp": "2023-11-29T13:06:33.549685303" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T15:16:36.337112514" + }, + "sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T10:08:55.434831174" }, "sarscov2 - [vcf, [], samples], fai": { "content": [ @@ -114,7 +397,13 @@ ] ], "1": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + + ], + "2": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ], + "index": [ + ], "vcf": [ [ @@ -126,11 +415,15 @@ ] ], "versions": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" ] } ], - "timestamp": "2023-11-29T13:06:23.474745156" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T09:52:12.216002665" }, "sarscov2 - [vcf, header, []], []": { "content": [ @@ -145,7 +438,13 @@ ] ], "1": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + + ], + "2": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ], + "index": [ + ], "vcf": [ [ @@ -157,10 +456,14 @@ ] ], "versions": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" ] } ], - "timestamp": "2023-11-29T13:06:13.841648691" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T09:51:54.062386022" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/reheader/tests/vcf_gz_index.config b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index.config new file mode 100644 index 00000000..1e050ec7 --- /dev/null +++ b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args2 = "--output-type z --write-index --no-version" +} diff --git a/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..536e4b42 --- /dev/null +++ b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args2 = "--output-type z --write-index=csi --no-version" +} diff --git a/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..91a80db7 --- /dev/null +++ b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_tbi.config @@ -0,0 +1,5 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args2 = "--output-type z --write-index=tbi --no-version" + +} diff --git a/modules/nf-core/bcftools/stats/environment.yml b/modules/nf-core/bcftools/stats/environment.yml index 1a969528..128fe204 100644 --- a/modules/nf-core/bcftools/stats/environment.yml +++ b/modules/nf-core/bcftools/stats/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index ffa1df64..20e5da77 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/stats/tests/main.nf.test b/modules/nf-core/bcftools/stats/tests/main.nf.test new file mode 100644 index 00000000..be618b0b --- /dev/null +++ b/modules/nf-core/bcftools/stats/tests/main.nf.test @@ -0,0 +1,182 @@ +nextflow_process { + + name "Test Process BCFTOOLS_STATS" + script "../main.nf" + process "BCFTOOLS_STATS" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/stats" + + test("sarscov2 - vcf_gz") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + []] + input[1] = [ [], [] ] + input[2] = [ [], [] ] + input[3] = [ [], [] ] + input[4] = [ [], [] ] + input[5] = [ [], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match("versions") }, + { assert snapshot(file(process.out.stats.get(0).get(1)).readLines()[0..5]).match() }, + ) + } + + } + + test("sarscov2 - vcf_gz - regions") { + + when { + process { + """ + input[0] = [ [ id:'regions_test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)] + input[1] = [ [id:'regions_test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) ] + input[2] = [ [], [] ] + input[3] = [ [], [] ] + input[4] = [ [], [] ] + input[5] = [ [], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match("regions_versions") }, + { assert snapshot(file(process.out.stats.get(0).get(1)).readLines()[0..5]).match() }, + ) + } + + } + + test("sarscov2 - vcf_gz - targets") { + + when { + process { + """ + input[0] = [ [ id:'targets_test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] ] + input[1] = [ [], [] ] + input[2] = [ [id:'targets_test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz', checkIfExists: true) + ] + input[3] = [ [], [] ] + input[4] = [ [], [] ] + input[5] = [ [], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match("targets_versions") }, + { assert snapshot(file(process.out.stats.get(0).get(1)).readLines()[0..5]).match() }, + ) + } + + } + + test("sarscov2 - vcf_gz - exons") { + + when { + process { + """ + input[0] = [ [ id:'exon_test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] ] + input[1] = [ [], [] ] + input[2] = [ [], [] ] + input[3] = [ [], [] ] + input[4] = [ [id: "exon_test"], + file(params.modules_testdata_base_path + 'delete_me/bcftools/stats/exons.tsv.gz', checkIfExists: true) ] + input[5] = [ [], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match("exon_versions") }, + { assert snapshot(file(process.out.stats.get(0).get(1)).readLines()[0..5]).match() }, + ) + } + + } + + test("sarscov2 - vcf_gz - reference") { + + when { + process { + """ + input[0] = [ [ id:'ref_test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] ] + input[1] = [ [], [] ] + input[2] = [ [], [] ] + input[3] = [ [], [] ] + input[4] = [ [], [] ] + input[5] = [ [id: 'ref_test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match("ref_versions") }, + { assert snapshot(file(process.out.stats.get(0).get(1)).readLines()[0..5]).match() }, + ) + } + + } + + + test("sarscov2 - vcf_gz - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + []] + input[1] = [ [], [] ] + input[2] = [ [], [] ] + input[3] = [ [], [] ] + input[4] = [ [], [] ] + input[5] = [ [], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/stats/tests/main.nf.test.snap b/modules/nf-core/bcftools/stats/tests/main.nf.test.snap new file mode 100644 index 00000000..cd8cff6d --- /dev/null +++ b/modules/nf-core/bcftools/stats/tests/main.nf.test.snap @@ -0,0 +1,180 @@ +{ + "sarscov2 - vcf_gz - reference": { + "content": [ + [ + "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.", + "# The command line was:\tbcftools stats --fasta-ref genome.fasta test.vcf.gz", + "#", + "# Definition of sets:", + "# ID\t[2]id\t[3]tab-separated file names", + "ID\t0\ttest.vcf.gz" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:14:35.506777837" + }, + "sarscov2 - vcf_gz - exons": { + "content": [ + [ + "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.", + "# The command line was:\tbcftools stats --exons exons.tsv.gz test.vcf.gz", + "#", + "# Definition of sets:", + "# ID\t[2]id\t[3]tab-separated file names", + "ID\t0\ttest.vcf.gz" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:14:30.57486244" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:16:27.637515559" + }, + "sarscov2 - vcf_gz - targets": { + "content": [ + [ + "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.", + "# The command line was:\tbcftools stats --targets-file test2.targets.tsv.gz test.vcf.gz", + "#", + "# Definition of sets:", + "# ID\t[2]id\t[3]tab-separated file names", + "ID\t0\ttest.vcf.gz" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:14:25.732997442" + }, + "regions_versions": { + "content": [ + [ + "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:16:32.559884458" + }, + "targets_versions": { + "content": [ + [ + "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:16:37.512009805" + }, + "sarscov2 - vcf_gz - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a" + ], + "stats": [ + [ + { + "id": "test" + }, + "test.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-03T11:57:09.614976125" + }, + "exon_versions": { + "content": [ + [ + "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:16:42.347397266" + }, + "ref_versions": { + "content": [ + [ + "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:16:47.26823622" + }, + "sarscov2 - vcf_gz": { + "content": [ + [ + "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.", + "# The command line was:\tbcftools stats test.vcf.gz", + "#", + "# Definition of sets:", + "# ID\t[2]id\t[3]tab-separated file names", + "ID\t0\ttest.vcf.gz" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:16:27.670416598" + }, + "sarscov2 - vcf_gz - regions": { + "content": [ + [ + "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.", + "# The command line was:\tbcftools stats --regions-file test3.vcf.gz test.vcf.gz", + "#", + "# Definition of sets:", + "# ID\t[2]id\t[3]tab-separated file names", + "ID\t0\ttest.vcf.gz" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:14:20.759094062" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/stats/tests/tags.yml b/modules/nf-core/bcftools/stats/tests/tags.yml new file mode 100644 index 00000000..53c12d92 --- /dev/null +++ b/modules/nf-core/bcftools/stats/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/stats: + - "modules/nf-core/bcftools/stats/**" diff --git a/modules/nf-core/ensemblvep/download/ensemblvep-download.diff b/modules/nf-core/ensemblvep/download/ensemblvep-download.diff deleted file mode 100644 index 954d28c3..00000000 --- a/modules/nf-core/ensemblvep/download/ensemblvep-download.diff +++ /dev/null @@ -1,25 +0,0 @@ -Changes in module 'nf-core/ensemblvep/download' ---- modules/nf-core/ensemblvep/download/main.nf -+++ modules/nf-core/ensemblvep/download/main.nf -@@ -4,8 +4,8 @@ - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : -- 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }" -+ 'https://depot.galaxyproject.org/singularity/ensembl-vep:105.0--pl5321h4a94de4_1' : -+ 'biocontainers/ensembl-vep:105.0--pl5321h4a94de4_1' }" - - input: - tuple val(meta), val(assembly), val(species), val(cache_version) - ---- modules/nf-core/ensemblvep/download/environment.yml -+++ modules/nf-core/ensemblvep/download/environment.yml -@@ -4,4 +4,4 @@ - - bioconda - - defaults - dependencies: -- - bioconda::ensembl-vep=110.0 -+ - bioconda::ensembl-vep=105.0 - -************************************************************ diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml index adba76e8..91564cce 100644 --- a/modules/nf-core/ensemblvep/download/environment.yml +++ b/modules/nf-core/ensemblvep/download/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::ensembl-vep=105.0 + - bioconda::ensembl-vep=112.0 diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf index f6ed5872..555c3c66 100644 --- a/modules/nf-core/ensemblvep/download/main.nf +++ b/modules/nf-core/ensemblvep/download/main.nf @@ -4,24 +4,25 @@ process ENSEMBLVEP_DOWNLOAD { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:105.0--pl5321h4a94de4_1' : - 'biocontainers/ensembl-vep:105.0--pl5321h4a94de4_1' }" + 'https://depot.galaxyproject.org/singularity/ensembl-vep:112.0--pl5321h2a3209d_0' : + 'biocontainers/ensembl-vep:112.0--pl5321h2a3209d_0' }" input: tuple val(meta), val(assembly), val(species), val(cache_version) output: - tuple val(meta), path("vep_cache"), emit: cache - path "versions.yml" , emit: versions + tuple val(meta), path(prefix), emit: cache + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: 'vep_cache' """ vep_install \\ - --CACHEDIR vep_cache \\ + --CACHEDIR $prefix \\ --SPECIES $species \\ --ASSEMBLY $assembly \\ --CACHE_VERSION $cache_version \\ @@ -34,8 +35,9 @@ process ENSEMBLVEP_DOWNLOAD { """ stub: + prefix = task.ext.prefix ?: 'vep_cache' """ - mkdir vep_cache + mkdir $prefix cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test b/modules/nf-core/ensemblvep/download/tests/main.nf.test new file mode 100644 index 00000000..ac41cc3f --- /dev/null +++ b/modules/nf-core/ensemblvep/download/tests/main.nf.test @@ -0,0 +1,60 @@ +nextflow_process { + + name "Test Process ENSEMBLVEP_DOWNLOAD" + script "../main.nf" + process "ENSEMBLVEP_DOWNLOAD" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "ensemblvep" + tag "ensemblvep/download" + + test("celegans - download") { + + when { + process { + """ + input[0] = Channel.of([ + [id:"112_WBcel235"], + params.vep_genome, + params.vep_species, + params.vep_cache_version + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("celegans - download - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [id:"112_WBcel235"], + params.vep_genome, + params.vep_species, + params.vep_cache_version + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap new file mode 100644 index 00000000..9e303c54 --- /dev/null +++ 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] + ], + "versions": [ + "versions.yml:md5,e32852e9cba2a298b7518ce610011b14" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-02T13:19:23.308683" + } +} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/download/tests/nextflow.config b/modules/nf-core/ensemblvep/download/tests/nextflow.config new file mode 100644 index 00000000..9aa48164 --- /dev/null +++ b/modules/nf-core/ensemblvep/download/tests/nextflow.config @@ -0,0 +1,12 @@ +params { + vep_cache_version = "112" + vep_genome = "WBcel235" + vep_species = "caenorhabditis_elegans" +} + +process { + withName: ENSEMBLVEP_DOWNLOAD { + ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' + ext.prefix = { "${params.vep_cache_version}_${params.vep_genome}" } + } +} diff --git a/modules/nf-core/ensemblvep/download/tests/tags.yml b/modules/nf-core/ensemblvep/download/tests/tags.yml new file mode 100644 index 00000000..26671f3d --- /dev/null +++ b/modules/nf-core/ensemblvep/download/tests/tags.yml @@ -0,0 +1,2 @@ +ensemblvep/download: + - "modules/nf-core/ensemblvep/download/**" diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index 3a9fbb4e..f180f749 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -8,12 +8,12 @@ process GATK4_GENOTYPEGVCFS { 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: - tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index) - path fasta - path fai - path dict - path dbsnp - path dbsnp_tbi + tuple val(meta), path(input), path(gvcf_index), path(intervals), path(intervals_index) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) + tuple val(meta5), path(dbsnp) + tuple val(meta6), path(dbsnp_tbi) output: tuple val(meta), path("*.vcf.gz"), emit: vcf @@ -26,7 +26,7 @@ process GATK4_GENOTYPEGVCFS { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def gvcf_command = gvcf.name.endsWith(".vcf") || gvcf.name.endsWith(".vcf.gz") ? "$gvcf" : "gendb://$gvcf" + def input_command = input.name.endsWith(".vcf") || input.name.endsWith(".vcf.gz") ? "$input" : "gendb://$input" def dbsnp_command = dbsnp ? "--dbsnp $dbsnp" : "" def interval_command = intervals ? "--intervals $intervals" : "" @@ -39,7 +39,7 @@ process GATK4_GENOTYPEGVCFS { """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ GenotypeGVCFs \\ - --variant $gvcf_command \\ + --variant $input_command \\ --output ${prefix}.vcf.gz \\ --reference $fasta \\ $interval_command \\ @@ -57,7 +57,7 @@ process GATK4_GENOTYPEGVCFS { def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf.gz + echo | gzip > ${prefix}.vcf.gz touch ${prefix}.vcf.gz.tbi cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff b/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff deleted file mode 100644 index 275b0dd0..00000000 --- a/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff +++ /dev/null @@ -1,16 +0,0 @@ -Changes in module 'nf-core/gatk4/haplotypecaller' ---- modules/nf-core/gatk4/haplotypecaller/main.nf -+++ modules/nf-core/gatk4/haplotypecaller/main.nf -@@ -12,8 +12,8 @@ - tuple val(meta2), path(fasta) - tuple val(meta3), path(fai) - tuple val(meta4), path(dict) -- tuple val(meta5), path(dbsnp) -- tuple val(meta6), path(dbsnp_tbi) -+ path(dbsnp) -+ path(dbsnp_tbi) - - output: - tuple val(meta), path("*.vcf.gz") , emit: vcf - -************************************************************ diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 7170169f..3043ee07 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -12,8 +12,8 @@ process GATK4_HAPLOTYPECALLER { tuple val(meta2), path(fasta) tuple val(meta3), path(fai) tuple val(meta4), path(dict) - path(dbsnp) - path(dbsnp_tbi) + tuple val(meta5), path(dbsnp) + tuple val(meta6), path(dbsnp_tbi) output: tuple val(meta), path("*.vcf.gz") , emit: vcf diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test index a124bff5..18d35f49 100644 --- a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test +++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test @@ -17,14 +17,14 @@ nextflow_process { """ input[0] = [ [ id:'test_bam' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [], [] ] - input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ] + input[1] = [ [ id:'test_fa' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'test_dict' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] input[4] = [ [], [] ] input[5] = [ [], [] ] @@ -35,9 +35,12 @@ nextflow_process { then { assertAll( { assert process.success }, - // { assert snapshot(process.out).match() }, // Unstable hashes - { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_bam_input") }, - { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_bam_input") }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.versions + ).match() + } ) } @@ -50,14 +53,14 @@ nextflow_process { """ input[0] = [ [ id:'test_cram' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [], [] ] - input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ] + input[1] = [ [ id:'test_fa' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'test_dict' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] input[4] = [ [], [] ] input[5] = [ [], [] ] """ @@ -67,9 +70,12 @@ nextflow_process { then { assertAll( { assert process.success }, - // { assert snapshot(process.out).match() }, // Unstable hashes - { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_input") }, - { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_input") }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.versions + ).match() + } ) } @@ -82,16 +88,16 @@ nextflow_process { """ input[0] = [ [ id:'test_cram_sites' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [], [] ] - input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ] - input[4] = [ [ id:'test_sites' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ] - input[5] = [ [ id:'test_sites_tbi' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) ] + input[1] = [ [ id:'test_fa' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'test_dict' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] + input[4] = [ [ id:'test_sites' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true) ] + input[5] = [ [ id:'test_sites_tbi' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true) ] """ } } @@ -99,9 +105,12 @@ nextflow_process { then { assertAll( { assert process.success }, - // { assert snapshot(process.out).match() }, // Unstable hashes - { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_input_with_sites") }, - { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_input_with_sites") }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.versions + ).match() + } ) } @@ -114,16 +123,16 @@ nextflow_process { """ input[0] = [ [ id:'test_cram_sites_dragstr' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_dragstrmodel'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt', checkIfExists: true) ] - input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ] - input[4] = [ [ id:'test_sites' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ] - input[5] = [ [ id:'test_sites_tbi' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) ] + input[1] = [ [ id:'test_fa' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'test_dict' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] + input[4] = [ [ id:'test_sites' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true) ] + input[5] = [ [ id:'test_sites_tbi' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true) ] """ } } @@ -131,9 +140,12 @@ nextflow_process { then { assertAll( { assert process.success }, - // { assert snapshot(process.out).match() }, // Unstable hashes - { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_dragstr_input_with_sites") }, - { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_dragstr_input_with_sites") }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.versions + ).match() + } ) } diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap index 375025ee..0203fcfc 100644 --- a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap @@ -1,82 +1,58 @@ { - "gatk_hc_vcf_cram_dragstr_input_with_sites": { + "homo_sapiens - [cram, crai] - fasta - fai - dict": { "content": [ - "test_cram_sites_dragstr.vcf.gz" + "test_cram.vcf.gz", + "test_cram.vcf.gz.tbi", + [ + "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-20T13:24:45.142682" + "timestamp": "2024-08-14T09:36:54.158605" }, - "gatk_hc_vcf_bam_input": { + "homo_sapiens - [cram, crai] - fasta - fai - dict - sites - sites_tbi": { "content": [ - "test_bam.vcf.gz" + "test_cram_sites.vcf.gz", + "test_cram_sites.vcf.gz.tbi", + [ + "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-20T13:23:19.203837" + "timestamp": "2024-08-14T09:37:13.77024" }, - "gatk_hc_vcf_cram_input": { + "homo_sapiens - [bam, bai] - fasta - fai - dict": { "content": [ - "test_cram.vcf.gz" + "test_bam.vcf.gz", + "test_bam.vcf.gz.tbi", + [ + "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-20T13:23:48.434615" + "timestamp": "2024-08-14T09:36:34.77631" }, - "gatk_hc_vcf_cram_input_with_sites": { + "homo_sapiens - [cram, crai, dragstr_model] - fasta - fai - dict - sites - sites_tbi": { "content": [ - "test_cram_sites.vcf.gz" + "test_cram_sites_dragstr.vcf.gz", + "test_cram_sites_dragstr.vcf.gz.tbi", + [ + "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-20T13:24:17.147745" - }, - "gatk_hc_vcf_tbi_bam_input": { - "content": [ - "test_bam.vcf.gz.tbi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-20T13:23:19.23048" - }, - "gatk_hc_vcf_tbi_cram_input": { - "content": [ - "test_cram.vcf.gz.tbi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-20T13:23:48.45958" - }, - "gatk_hc_vcf_tbi_cram_dragstr_input_with_sites": { - "content": [ - "test_cram_sites_dragstr.vcf.gz.tbi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-20T13:24:45.154818" - }, - "gatk_hc_vcf_tbi_cram_input_with_sites": { - "content": [ - "test_cram_sites.vcf.gz.tbi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-20T13:24:17.158138" + "timestamp": "2024-08-14T09:37:32.967085" } } \ No newline at end of file diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml index 34513c7f..3d98a08b 100644 --- a/modules/nf-core/gawk/environment.yml +++ b/modules/nf-core/gawk/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - anaconda::gawk=5.1.0 + - conda-forge::gawk=5.3.0 diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf index f856a1f8..ca468929 100644 --- a/modules/nf-core/gawk/main.nf +++ b/modules/nf-core/gawk/main.nf @@ -4,8 +4,8 @@ process GAWK { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gawk:5.1.0' : - 'biocontainers/gawk:5.1.0' }" + 'https://depot.galaxyproject.org/singularity/gawk:5.3.0' : + 'biocontainers/gawk:5.3.0' }" input: tuple val(meta), path(input) @@ -41,10 +41,11 @@ process GAWK { stub: prefix = task.ext.prefix ?: "${meta.id}" - suffix = task.ext.suffix ?: "${input.getExtension}" + suffix = task.ext.suffix ?: "${input.getExtension()}" + def create_cmd = suffix.endsWith("gz") ? "echo '' | gzip >" : "touch" """ - touch ${prefix}.${suffix} + ${create_cmd} ${prefix}.${suffix} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/gawk/tests/main.nf.test b/modules/nf-core/gawk/tests/main.nf.test new file mode 100644 index 00000000..fce82ca9 --- /dev/null +++ b/modules/nf-core/gawk/tests/main.nf.test @@ -0,0 +1,56 @@ +nextflow_process { + + name "Test Process GAWK" + script "../main.nf" + process "GAWK" + + tag "modules" + tag "modules_nfcore" + tag "gawk" + + test("convert fasta to bed") { + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("convert fasta to bed with program file") { + config "./nextflow_with_program_file.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = Channel.of('BEGIN {FS="\t"}; {print \$1 FS "0" FS \$2}').collectFile(name:"program.txt") + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/gawk/tests/main.nf.test.snap b/modules/nf-core/gawk/tests/main.nf.test.snap new file mode 100644 index 00000000..4f3a759c --- /dev/null +++ b/modules/nf-core/gawk/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "convert fasta to bed with program file": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-05-17T15:20:02.495430346" + }, + "convert fasta to bed": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-05-17T15:19:53.291809648" + } +} \ No newline at end of file diff --git a/modules/nf-core/gawk/tests/nextflow.config b/modules/nf-core/gawk/tests/nextflow.config new file mode 100644 index 00000000..6e5d43a3 --- /dev/null +++ b/modules/nf-core/gawk/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + withName: GAWK { + ext.suffix = "bed" + ext.args2 = '\'BEGIN {FS="\t"}; {print \$1 FS "0" FS \$2}\'' + } +} diff --git a/modules/nf-core/gawk/tests/nextflow_with_program_file.config b/modules/nf-core/gawk/tests/nextflow_with_program_file.config new file mode 100644 index 00000000..693ad419 --- /dev/null +++ b/modules/nf-core/gawk/tests/nextflow_with_program_file.config @@ -0,0 +1,5 @@ +process { + withName: GAWK { + ext.suffix = "bed" + } +} diff --git a/modules/nf-core/gawk/tests/tags.yml b/modules/nf-core/gawk/tests/tags.yml new file mode 100644 index 00000000..72e4531d --- /dev/null +++ b/modules/nf-core/gawk/tests/tags.yml @@ -0,0 +1,2 @@ +gawk: + - "modules/nf-core/gawk/**" diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml index 88c7126c..bcb9d64a 100644 --- a/modules/nf-core/mosdepth/environment.yml +++ b/modules/nf-core/mosdepth/environment.yml @@ -5,4 +5,4 @@ channels: - defaults dependencies: # renovate: datasource=conda depName=bioconda/mosdepth - - mosdepth=0.3.6 + - mosdepth=0.3.8 diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index c7e24303..6f4a8383 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -4,8 +4,8 @@ process MOSDEPTH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.6--hd299d5a_0' : - 'biocontainers/mosdepth:0.3.6--hd299d5a_0'}" + 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.8--hd299d5a_0' : + 'biocontainers/mosdepth:0.3.8--hd299d5a_0'}" input: tuple val(meta), path(bam), path(bai), path(bed) @@ -63,13 +63,13 @@ process MOSDEPTH { touch ${prefix}.region.dist.txt touch ${prefix}.summary.txt touch ${prefix}.per-base.d4 - touch ${prefix}.per-base.bed.gz + echo "" | gzip > ${prefix}.per-base.bed.gz touch ${prefix}.per-base.bed.gz.csi - touch ${prefix}.regions.bed.gz + echo "" | gzip > ${prefix}.regions.bed.gz touch ${prefix}.regions.bed.gz.csi - touch ${prefix}.quantized.bed.gz + echo "" | gzip > ${prefix}.quantized.bed.gz touch ${prefix}.quantized.bed.gz.csi - touch ${prefix}.thresholds.bed.gz + echo "" | gzip > ${prefix}.thresholds.bed.gz touch ${prefix}.thresholds.bed.gz.csi cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/mosdepth/tests/main.nf.test b/modules/nf-core/mosdepth/tests/main.nf.test index d991f819..0b3c860d 100644 --- a/modules/nf-core/mosdepth/tests/main.nf.test +++ b/modules/nf-core/mosdepth/tests/main.nf.test @@ -15,8 +15,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] ] input[1] = [[],[]] @@ -40,9 +40,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [[],[]] """ @@ -65,13 +65,13 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [] ] input[1] = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] """ } @@ -93,13 +93,13 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] """ } @@ -122,8 +122,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] ] input[1] = [[],[]] @@ -148,8 +148,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] ] input[1] = [[],[]] @@ -174,9 +174,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [[],[]] """ @@ -200,9 +200,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [[],[]] """ @@ -225,9 +225,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [[],[]] """ @@ -237,21 +237,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.global_txt[0][1]).name, - file(process.out.summary_txt[0][1]).name, - file(process.out.regions_txt[0][1]).name, - file(process.out.per_base_d4[0][1]).name, - file(process.out.per_base_bed[0][1]).name, - file(process.out.per_base_csi[0][1]).name, - file(process.out.regions_bed[0][1]).name, - file(process.out.regions_csi[0][1]).name, - file(process.out.quantized_bed[0][1]).name, - file(process.out.quantized_csi[0][1]).name, - file(process.out.thresholds_bed[0][1]).name, - file(process.out.thresholds_csi[0][1]).name, - process.out.versions - ).match() } + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/mosdepth/tests/main.nf.test.snap b/modules/nf-core/mosdepth/tests/main.nf.test.snap index dc4d9508..c604540b 100644 --- a/modules/nf-core/mosdepth/tests/main.nf.test.snap +++ b/modules/nf-core/mosdepth/tests/main.nf.test.snap @@ -1,23 +1,236 @@ { "homo_sapiens - bam, bai, [] - stub": { "content": [ - "test.global.dist.txt", - "test.summary.txt", - "test.region.dist.txt", - "test.per-base.d4", - "test.per-base.bed.gz", - "test.per-base.bed.gz.csi", - "test.regions.bed.gz", - "test.regions.bed.gz.csi", - "test.quantized.bed.gz", - "test.quantized.bed.gz.csi", - "test.thresholds.bed.gz", - "test.thresholds.bed.gz.csi", - [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.global.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + [ + { + "id": "test", + "single_end": true + }, + "test.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "11": [ + [ + { + "id": "test", + "single_end": true + }, + "test.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "12": [ + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + ], + "2": [ + [ + { + "id": "test", + "single_end": true + }, + "test.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + [ + { + "id": "test", + "single_end": true + }, + "test.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "7": [ + [ + { + "id": "test", + "single_end": true + }, + "test.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + { + "id": "test", + "single_end": true + }, + "test.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "9": [ + [ + { + "id": "test", + "single_end": true + }, + "test.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "global_txt": [ + [ + { + "id": "test", + "single_end": true + }, + "test.global.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "per_base_bed": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "per_base_csi": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "per_base_d4": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "quantized_bed": [ + [ + { + "id": "test", + "single_end": true + }, + "test.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "quantized_csi": [ + [ + { + "id": "test", + "single_end": true + }, + "test.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "regions_bed": [ + [ + { + "id": "test", + "single_end": true + }, + "test.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "regions_csi": [ + [ + { + "id": "test", + "single_end": true + }, + "test.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "regions_txt": [ + [ + { + "id": "test", + "single_end": true + }, + "test.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "summary_txt": [ + [ + { + "id": "test", + "single_end": true + }, + "test.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "thresholds_bed": [ + [ + { + "id": "test", + "single_end": true + }, + "test.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "thresholds_csi": [ + [ + { + "id": "test", + "single_end": true + }, + "test.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + ] + } ], - "timestamp": "2023-11-27T15:14:34.897155161" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:33:16.953408231" }, "homo_sapiens - cram, crai, bed": { "content": [ @@ -47,7 +260,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -67,7 +280,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -76,7 +289,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -85,7 +298,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "7": [ @@ -94,7 +307,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "8": [ @@ -118,7 +331,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -127,7 +340,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -145,7 +358,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "regions_csi": [ @@ -154,7 +367,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "regions_txt": [ @@ -182,11 +395,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:47:18.171150781" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:32:50.160217828" }, "homo_sapiens - bam, bai, [] - quantized": { "content": [ @@ -216,7 +433,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ @@ -230,7 +447,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -239,7 +456,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -254,7 +471,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz:md5,3e434a8bafcf59a67841ae3d4d752838" + "test.quantized.bed.gz:md5,f037c215449d361112efc10108fcc17c" ] ], "9": [ @@ -263,7 +480,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93" + "test.quantized.bed.gz.csi:md5,4f69e6ace50206a2768be66ded3a56f0" ] ], "global_txt": [ @@ -281,7 +498,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -290,7 +507,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -302,7 +519,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz:md5,3e434a8bafcf59a67841ae3d4d752838" + "test.quantized.bed.gz:md5,f037c215449d361112efc10108fcc17c" ] ], "quantized_csi": [ @@ -311,7 +528,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93" + "test.quantized.bed.gz.csi:md5,4f69e6ace50206a2768be66ded3a56f0" ] ], "regions_bed": [ @@ -339,11 +556,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:47:29.228103864" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:33:01.164885111" }, "homo_sapiens - bam, bai, bed": { "content": [ @@ -373,7 +594,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -393,7 +614,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -402,7 +623,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -411,7 +632,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "7": [ @@ -420,7 +641,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "8": [ @@ -444,7 +665,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -453,7 +674,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -471,7 +692,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "regions_csi": [ @@ -480,7 +701,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "regions_txt": [ @@ -508,11 +729,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:47:04.537716314" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:32:39.071657456" }, "homo_sapiens - bam, bai, [] - window": { "content": [ @@ -542,7 +767,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -550,7 +775,7 @@ "id": "test", "single_end": true }, - "test.mosdepth.region.dist.txt:md5,39e0e707ec32feb5176fd20a95f1f468" + "test.mosdepth.region.dist.txt:md5,0b6ea9f0da1228252d9aef2d3b6f7f76" ] ], "3": [ @@ -562,7 +787,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -571,7 +796,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -580,7 +805,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,f02e2cb49cc050e13d76942d6960827a" + "test.regions.bed.gz:md5,34f48d16fcdd61e44d812e29e02c77b8" ] ], "7": [ @@ -589,7 +814,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d" + "test.regions.bed.gz.csi:md5,2a30bcb7f5c7632136b3efce24723970" ] ], "8": [ @@ -613,7 +838,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -622,7 +847,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -640,7 +865,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,f02e2cb49cc050e13d76942d6960827a" + "test.regions.bed.gz:md5,34f48d16fcdd61e44d812e29e02c77b8" ] ], "regions_csi": [ @@ -649,7 +874,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d" + "test.regions.bed.gz.csi:md5,2a30bcb7f5c7632136b3efce24723970" ] ], "regions_txt": [ @@ -658,7 +883,7 @@ "id": "test", "single_end": true }, - "test.mosdepth.region.dist.txt:md5,39e0e707ec32feb5176fd20a95f1f468" + "test.mosdepth.region.dist.txt:md5,0b6ea9f0da1228252d9aef2d3b6f7f76" ] ], "summary_txt": [ @@ -677,11 +902,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:47:23.708536171" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:32:55.631776118" }, "homo_sapiens - bam, bai, []": { "content": [ @@ -711,7 +940,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ @@ -725,7 +954,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -734,7 +963,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -764,7 +993,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -773,7 +1002,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -810,11 +1039,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:46:56.975710077" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:32:33.642125299" }, "homo_sapiens - cram, crai, []": { "content": [ @@ -844,7 +1077,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ @@ -858,7 +1091,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -867,7 +1100,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -897,7 +1130,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -906,7 +1139,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -943,11 +1176,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:47:12.09259995" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:32:44.704920941" }, "homo_sapiens - bam, bai, bed - thresholds": { "content": [ @@ -976,7 +1213,7 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz:md5,13101e326eea3cbfa1d569b69f494f4c" + "test.thresholds.bed.gz:md5,fe70ae728cd10726c42a2bcd44adfc9d" ] ], "11": [ @@ -985,11 +1222,11 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196" + "test.thresholds.bed.gz.csi:md5,219414a0751185adb98d2235d83ea055" ] ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -1009,7 +1246,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -1018,7 +1255,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -1027,7 +1264,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "7": [ @@ -1036,7 +1273,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "8": [ @@ -1060,7 +1297,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -1069,7 +1306,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -1087,7 +1324,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "regions_csi": [ @@ -1096,7 +1333,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "regions_txt": [ @@ -1123,7 +1360,7 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz:md5,13101e326eea3cbfa1d569b69f494f4c" + "test.thresholds.bed.gz:md5,fe70ae728cd10726c42a2bcd44adfc9d" ] ], "thresholds_csi": [ @@ -1132,14 +1369,18 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196" + "test.thresholds.bed.gz.csi:md5,219414a0751185adb98d2235d83ea055" ] ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:49:44.311847326" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:33:06.737266831" } } \ No newline at end of file diff --git a/modules/nf-core/rtgtools/pedfilter/main.nf b/modules/nf-core/rtgtools/pedfilter/main.nf index bb36cf50..f6486e17 100644 --- a/modules/nf-core/rtgtools/pedfilter/main.nf +++ b/modules/nf-core/rtgtools/pedfilter/main.nf @@ -11,8 +11,8 @@ process RTGTOOLS_PEDFILTER { tuple val(meta), path(input) output: - tuple val(meta), path("*.vcf.gz") , emit: output - path "versions.yml" , emit: versions + tuple val(meta), path("*.{vcf.gz,ped}") , emit: output + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -31,12 +31,10 @@ process RTGTOOLS_PEDFILTER { def postprocess = extension == "vcf.gz" ? "| rtg bgzip ${args2} -" : "" """ - cut -f1-6 ${input} > ${prefix}.ped - rtg pedfilter \\ ${args} \\ - ${prefix}.ped \\ - | head -n -1 ${postprocess} > ${prefix}.${extension} + ${input} \\ + ${postprocess} > ${prefix}.${extension} cat <<-END_VERSIONS > versions.yml @@ -46,7 +44,6 @@ process RTGTOOLS_PEDFILTER { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def extension = args.contains("--vcf") ? "vcf.gz" : "ped" diff --git a/modules/nf-core/rtgtools/pedfilter/meta.yml b/modules/nf-core/rtgtools/pedfilter/meta.yml index 785ac990..4e90fd7b 100644 --- a/modules/nf-core/rtgtools/pedfilter/meta.yml +++ b/modules/nf-core/rtgtools/pedfilter/meta.yml @@ -11,7 +11,7 @@ tools: homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" - licence: "['BSD']" + licence: ["BSD"] input: - meta: type: map diff --git a/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff b/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff deleted file mode 100644 index 4463e941..00000000 --- a/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff +++ /dev/null @@ -1,39 +0,0 @@ -Changes in module 'nf-core/rtgtools/pedfilter' ---- modules/nf-core/rtgtools/pedfilter/main.nf -+++ modules/nf-core/rtgtools/pedfilter/main.nf -@@ -11,8 +11,8 @@ - tuple val(meta), path(input) - - output: -- tuple val(meta), path("*.{vcf.gz,ped}") , emit: output -- path "versions.yml" , emit: versions -+ tuple val(meta), path("*.vcf.gz") , emit: output -+ path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when -@@ -31,10 +31,12 @@ - def postprocess = extension == "vcf.gz" ? "| rtg bgzip ${args2} -" : "" - - """ -+ cut -f1-6 ${input} > ${prefix}.ped -+ - rtg pedfilter \\ - ${args} \\ -- ${input} \\ -- ${postprocess} > ${prefix}.${extension} -+ ${prefix}.ped \\ -+ | head -n -1 ${postprocess} > ${prefix}.${extension} - - - cat <<-END_VERSIONS > versions.yml -@@ -44,6 +46,7 @@ - """ - - stub: -+ def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - - def extension = args.contains("--vcf") ? "vcf.gz" : "ped" - -************************************************************ diff --git a/modules/nf-core/rtgtools/pedfilter/tests/main.nf.test b/modules/nf-core/rtgtools/pedfilter/tests/main.nf.test new file mode 100644 index 00000000..0ddcebdb --- /dev/null +++ b/modules/nf-core/rtgtools/pedfilter/tests/main.nf.test @@ -0,0 +1,85 @@ + +nextflow_process { + + name "Test Process RTGTOOLS_PEDFILTER" + script "../main.nf" + process "RTGTOOLS_PEDFILTER" + + tag "modules" + tag "modules_nfcore" + tag "rtgtools" + tag "rtgtools/pedfilter" + + test("test-rtgtools-pedfilter-ped") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-rtgtools-pedfilter-vcf") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-rtgtools-pedfilter-vcf-output") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.output[0][1]).linesGzip[3..7], + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/rtgtools/pedfilter/tests/main.nf.test.snap b/modules/nf-core/rtgtools/pedfilter/tests/main.nf.test.snap new file mode 100644 index 00000000..7475fa8b --- /dev/null +++ b/modules/nf-core/rtgtools/pedfilter/tests/main.nf.test.snap @@ -0,0 +1,91 @@ +{ + "test-rtgtools-pedfilter-vcf": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped:md5,342135c8bf22e573367b75ef5e1c5e6b" + ] + ], + "1": [ + "versions.yml:md5,036d97d5be26fce2e7d956034b9dc86d" + ], + "output": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped:md5,342135c8bf22e573367b75ef5e1c5e6b" + ] + ], + "versions": [ + "versions.yml:md5,036d97d5be26fce2e7d956034b9dc86d" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T16:11:01.797205" + }, + "test-rtgtools-pedfilter-vcf-output": { + "content": [ + [ + "##CL=pedfilter --vcf justhusky.ped", + "##diseased=hugelymodelbat", + "##SAMPLE=", + "##SAMPLE=", + "##SAMPLE=" + ], + [ + "versions.yml:md5,036d97d5be26fce2e7d956034b9dc86d" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T20:46:00.069224" + }, + "test-rtgtools-pedfilter-ped": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped:md5,a8b8f6538e1738d6e06fddfe15d36f09" + ] + ], + "1": [ + "versions.yml:md5,036d97d5be26fce2e7d956034b9dc86d" + ], + "output": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped:md5,a8b8f6538e1738d6e06fddfe15d36f09" + ] + ], + "versions": [ + "versions.yml:md5,036d97d5be26fce2e7d956034b9dc86d" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T16:10:53.473351" + } +} \ No newline at end of file diff --git a/modules/nf-core/rtgtools/pedfilter/tests/nextflow.config b/modules/nf-core/rtgtools/pedfilter/tests/nextflow.config new file mode 100644 index 00000000..a8a3ec54 --- /dev/null +++ b/modules/nf-core/rtgtools/pedfilter/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'RTGTOOLS_PEDFILTER' { + ext.args = "--vcf" + } +} diff --git a/modules/nf-core/rtgtools/rocplot/meta.yml b/modules/nf-core/rtgtools/rocplot/meta.yml index 927cff90..2b4d43d7 100644 --- a/modules/nf-core/rtgtools/rocplot/meta.yml +++ b/modules/nf-core/rtgtools/rocplot/meta.yml @@ -11,7 +11,7 @@ tools: homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" - licence: "['BSD']" + licence: ["BSD"] input: - meta: type: map diff --git a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test index 160eafcf..c7c37084 100644 --- a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test +++ b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test @@ -7,6 +7,8 @@ nextflow_process { tag "modules_nfcore" tag "rtgtools" tag "rtgtools/rocplot" + tag "rtgtools/vcfeval" + tag "untar" test("homo_sapiens - tsv") { @@ -17,7 +19,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_21_sdf']) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome_sdf.tar.gz', checkIfExists: true) ] """ } @@ -29,12 +31,12 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = UNTAR.out.untar println(projectDir) diff --git a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test.snap b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test.snap index 389ffb5b..f4dee3a1 100644 --- a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test.snap +++ b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test.snap @@ -5,6 +5,10 @@ "test.svg", "versions.yml" ], - "timestamp": "2023-10-24T12:48:36.35343056" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-09T10:44:42.642303" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml index cd4ee8c3..7a95ca61 100644 --- a/modules/nf-core/samtools/convert/environment.yml +++ b/modules/nf-core/samtools/convert/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index e2d679f7..03b7b525 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_CONVERT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(input), path(index) @@ -13,8 +13,11 @@ process SAMTOOLS_CONVERT { tuple val(meta3), path(fai) output: - tuple val(meta), path("*.{cram,bam}"), path("*.{crai,bai}") , emit: alignment_index - path "versions.yml" , emit: versions + tuple val(meta), path("*.bam") , emit: bam , optional: true + tuple val(meta), path("*.cram") , emit: cram, optional: true + tuple val(meta), path("*.bai") , emit: bai , optional: true + tuple val(meta), path("*.crai") , emit: crai, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -39,4 +42,19 @@ process SAMTOOLS_CONVERT { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def output_extension = input.getExtension() == "bam" ? "cram" : "bam" + def index_extension = output_extension == "bam" ? "bai" : "crai" + + """ + touch ${prefix}.${output_extension} + touch ${prefix}.${index_extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/samtools/convert/meta.yml b/modules/nf-core/samtools/convert/meta.yml index f8a1612f..55828971 100644 --- a/modules/nf-core/samtools/convert/meta.yml +++ b/modules/nf-core/samtools/convert/meta.yml @@ -39,10 +39,22 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - alignment_index: + - bam: type: file - description: filtered/converted BAM/CRAM file + index - pattern: "*{.bam/cram,.bai/crai}" + description: filtered/converted BAM file + pattern: "*{.bam}" + - cram: + type: file + description: filtered/converted CRAM file + pattern: "*{cram}" + - bai: + type: file + description: filtered/converted BAM index + pattern: "*{.bai}" + - crai: + type: file + description: filtered/converted CRAM index + pattern: "*{.crai}" - version: type: file description: File containing software version @@ -53,3 +65,4 @@ authors: maintainers: - "@FriederikeHanssen" - "@maxulysse" + - "@matthdsm" diff --git a/modules/nf-core/samtools/convert/tests/main.nf.test b/modules/nf-core/samtools/convert/tests/main.nf.test index ee59532a..91a0c69e 100644 --- a/modules/nf-core/samtools/convert/tests/main.nf.test +++ b/modules/nf-core/samtools/convert/tests/main.nf.test @@ -34,9 +34,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.alignment_index[0][1]).name).match("bam_alignment_index_1") }, - { assert snapshot(file(process.out.alignment_index[0][2]).name).match("bam_alignment_index_2") }, - { assert snapshot(process.out.versions).match("bam_versions") } + { assert snapshot(file(process.out.cram[0][1]).name).match("bam_to_cram_alignment") }, + { assert snapshot(file(process.out.crai[0][1]).name).match("bam_to_cram_index") }, + { assert snapshot(process.out.versions).match("bam_to_cram_versions") } ) } } @@ -66,9 +66,41 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.alignment_index[0][1]).name).match("cram_alignment_index_1") }, - { assert snapshot(file(process.out.alignment_index[0][2]).name).match("cram_alignment_index_2") }, - { assert snapshot(process.out.versions).match("cram_versions") } + { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_alignment") }, + { assert snapshot(file(process.out.bai[0][1]).name).match("cram_to_bam_alignment_index") }, + { assert snapshot(process.out.versions).match("cram_to_bam_versions") } + ) + } + } + + test("sarscov2 - [bam, bai], fasta, fai - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'fai' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match("stub") } ) } } diff --git a/modules/nf-core/samtools/convert/tests/main.nf.test.snap b/modules/nf-core/samtools/convert/tests/main.nf.test.snap index 96ec9f4e..51362902 100644 --- a/modules/nf-core/samtools/convert/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/convert/tests/main.nf.test.snap @@ -1,66 +1,131 @@ { - "cram_alignment_index_1": { + "cram_to_bam_alignment": { "content": [ "test.bam" ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-02T17:04:16.431159" + "timestamp": "2024-03-06T11:14:51.300147176" }, - "cram_alignment_index_2": { + "bam_to_cram_alignment": { "content": [ - "test.bam.bai" + "test.cram" ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-02T17:04:16.43428" + "timestamp": "2024-03-06T11:14:36.625470184" }, - "bam_alignment_index_2": { + "cram_to_bam_versions": { "content": [ - "test.cram.crai" + [ + "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-02T17:00:29.669534" + "timestamp": "2024-05-28T15:44:34.618037105" }, - "bam_alignment_index_1": { + "bam_to_cram_versions": { "content": [ - "test.cram" + [ + "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-02T17:00:29.666821" + "timestamp": "2024-05-28T15:44:29.165839679" }, - "cram_versions": { + "stub": { "content": [ - [ - "versions.yml:md5,dd0aaf61f39c9ce91c74090f3c7ce1d0" - ] + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" + ], + "bai": [ + + ], + "bam": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" + ] + } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:14:38.224641326" + "timestamp": "2024-05-28T15:44:40.258233921" }, - "bam_versions": { + "bam_to_cram_index": { "content": [ - [ - "versions.yml:md5,dd0aaf61f39c9ce91c74090f3c7ce1d0" - ] + "test.cram.crai" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-06T11:14:36.640009334" + }, + "cram_to_bam_alignment_index": { + "content": [ + "test.bam.bai" ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:14:29.852388191" + "timestamp": "2024-03-06T11:14:51.304477426" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index 3e95dd71..f8450fa5 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -1,8 +1,10 @@ name: samtools_faidx + channels: - conda-forge - bioconda - defaults + dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index cfe7ad95..bdcdbc95 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FAIDX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index e189af28..f3c25de2 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -39,6 +39,10 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + - fa: + type: file + description: FASTA file + pattern: "*.{fa}" - fai: type: file description: FASTA index file diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test new file mode 100644 index 00000000..17244ef2 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test @@ -0,0 +1,122 @@ +nextflow_process { + + name "Test Process SAMTOOLS_FAIDX" + script "../main.nf" + process "SAMTOOLS_FAIDX" + + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/faidx" + + test("test_samtools_faidx") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_bgzip") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_fasta") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_stub_fasta") { + + config "./nextflow2.config" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_stub_fai") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap new file mode 100644 index 00000000..3223b72b --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -0,0 +1,249 @@ +{ + "test_samtools_faidx": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:14.779784761" + }, + "test_samtools_faidx_bgzip": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" + ] + ], + "3": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" + ] + ], + "versions": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:20.256633877" + }, + "test_samtools_faidx_fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ], + "fa": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36" + ] + ], + "fai": [ + + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:25.632577273" + }, + "test_samtools_faidx_stub_fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ], + "fa": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "fai": [ + + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:31.058424849" + }, + "test_samtools_faidx_stub_fai": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:36.479929617" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/tests/nextflow.config b/modules/nf-core/samtools/faidx/tests/nextflow.config new file mode 100644 index 00000000..f76a3ba0 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: SAMTOOLS_FAIDX { + ext.args = 'MT192765.1 -o extract.fa' + } + +} diff --git a/modules/nf-core/samtools/faidx/tests/nextflow2.config b/modules/nf-core/samtools/faidx/tests/nextflow2.config new file mode 100644 index 00000000..33ebbd5d --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/nextflow2.config @@ -0,0 +1,6 @@ +process { + + withName: SAMTOOLS_FAIDX { + ext.args = '-o extract.fa' + } +} diff --git a/modules/nf-core/samtools/faidx/tests/tags.yml b/modules/nf-core/samtools/faidx/tests/tags.yml new file mode 100644 index 00000000..e4a83948 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/faidx: + - modules/nf-core/samtools/faidx/** diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index a5e50649..260d516b 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index dc14f98d..e002585b 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(input) @@ -35,10 +35,11 @@ process SAMTOOLS_INDEX { """ stub: + def args = task.ext.args ?: '' + def extension = file(input).getExtension() == 'cram' ? + "crai" : args.contains("-c") ? "csi" : "bai" """ - touch ${input}.bai - touch ${input}.crai - touch ${input}.csi + touch ${input}.${extension} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test index bb7756d1..ca34fb5c 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -9,11 +9,7 @@ nextflow_process { tag "samtools/index" test("bai") { - when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -27,18 +23,13 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.bai).match("bai") }, - { assert snapshot(process.out.versions).match("bai_versions") } + { assert snapshot(process.out).match() } ) } } test("crai") { - when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -52,20 +43,83 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.crai).match("crai") }, - { assert snapshot(process.out.versions).match("crai_versions") } + { assert snapshot(process.out).match() } ) } } test("csi") { - config "./csi.nextflow.config" when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.csi[0][1]).name, + process.out.versions + ).match() } + ) + } + } + + test("bai - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("crai - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) + ]) + """ } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("csi - stub") { + options "-stub" + config "./csi.nextflow.config" + + when { process { """ input[0] = Channel.of([ @@ -79,8 +133,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert path(process.out.csi.get(0).get(1)).exists() }, - { assert snapshot(process.out.versions).match("csi_versions") } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 3dc8e7de..799d199c 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -1,74 +1,250 @@ { - "crai_versions": { + "csi - stub": { "content": [ - [ - "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" - ] + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + + ], + "crai": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-13T16:12:00.324667957" + "timestamp": "2024-07-22T16:51:53.9057" }, - "csi_versions": { + "crai - stub": { "content": [ - [ - "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" - ] + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-13T16:12:07.885103162" + "timestamp": "2024-07-22T16:51:45.931558" }, - "crai": { + "bai - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "crai": [ + + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-12T18:41:38.446424" + "timestamp": "2024-07-22T16:51:34.807525" }, - "bai": { + "csi": { "content": [ + "test.paired_end.sorted.bam.csi", [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" - ] + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-12T18:40:46.579747" + "timestamp": "2024-07-22T16:52:55.688799" }, - "bai_versions": { + "crai": { "content": [ - [ - "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" - ] + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T16:51:17.609533" + }, + "bai": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ], + "crai": [ + + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-13T16:11:51.641425452" + "timestamp": "2024-07-22T16:51:04.16585" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml index fc669b1b..cd366d6d 100644 --- a/modules/nf-core/samtools/merge/environment.yml +++ b/modules/nf-core/samtools/merge/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index a3048c28..693b1d80 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_MERGE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(input_files, stageAs: "?/*") diff --git a/modules/nf-core/samtools/merge/samtools-merge.diff b/modules/nf-core/samtools/merge/samtools-merge.diff deleted file mode 100644 index 59077e1f..00000000 --- a/modules/nf-core/samtools/merge/samtools-merge.diff +++ /dev/null @@ -1,13 +0,0 @@ -Changes in module 'nf-core/samtools/merge' ---- modules/nf-core/samtools/merge/main.nf -+++ modules/nf-core/samtools/merge/main.nf -@@ -1,6 +1,6 @@ - process SAMTOOLS_MERGE { - tag "$meta.id" -- label 'process_low' -+ label 'process_high' - - conda "bioconda::samtools=1.17" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - -************************************************************ diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test.snap b/modules/nf-core/samtools/merge/tests/main.nf.test.snap index f7da7699..17bc846f 100644 --- a/modules/nf-core/samtools/merge/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/merge/tests/main.nf.test.snap @@ -80,14 +80,14 @@ "bam_versions": { "content": [ [ - "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4" + "versions.yml:md5,84dab54b9812780df48f5cecef690c34" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:16:33.782637377" + "timestamp": "2024-05-28T15:46:35.851936597" }, "bams_csi": { "content": [ @@ -124,14 +124,14 @@ "bams_stub_versions": { "content": [ [ - "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4" + "versions.yml:md5,84dab54b9812780df48f5cecef690c34" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:16:42.594476052" + "timestamp": "2024-05-28T15:46:41.405707643" }, "bam_cram": { "content": [ @@ -158,14 +158,14 @@ "bams_versions": { "content": [ [ - "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4" + "versions.yml:md5,84dab54b9812780df48f5cecef690c34" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:16:04.805335656" + "timestamp": "2024-05-28T15:45:51.695689923" }, "crams_bam": { "content": [ @@ -182,14 +182,14 @@ "crams_versions": { "content": [ [ - "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4" + "versions.yml:md5,84dab54b9812780df48f5cecef690c34" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:16:25.889394689" + "timestamp": "2024-05-28T15:46:30.185392319" }, "bam_csi": { "content": [ diff --git a/modules/nf-core/somalier/extract/environment.yml b/modules/nf-core/somalier/extract/environment.yml index e0dd11c9..72397774 100644 --- a/modules/nf-core/somalier/extract/environment.yml +++ b/modules/nf-core/somalier/extract/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::somalier=0.2.15 + - bioconda::somalier=0.2.19 diff --git a/modules/nf-core/somalier/extract/main.nf b/modules/nf-core/somalier/extract/main.nf index 8dc3c31c..703605d1 100644 --- a/modules/nf-core/somalier/extract/main.nf +++ b/modules/nf-core/somalier/extract/main.nf @@ -5,14 +5,14 @@ process SOMALIER_EXTRACT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/somalier:0.2.15--h37c5b7d_0': - 'biocontainers/somalier:0.2.15--h37c5b7d_0' }" + 'https://depot.galaxyproject.org/singularity/somalier:0.2.19--h0c29559_0': + 'biocontainers/somalier:0.2.19--h0c29559_0' }" input: tuple val(meta), path(input), path(input_index) - path(fasta) - path(fai) - path(sites) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(sites) output: tuple val(meta), path("*.somalier") , emit: extract diff --git a/modules/nf-core/somalier/extract/meta.yml b/modules/nf-core/somalier/extract/meta.yml index 7aa426ab..aabaf5d6 100644 --- a/modules/nf-core/somalier/extract/meta.yml +++ b/modules/nf-core/somalier/extract/meta.yml @@ -19,7 +19,7 @@ tools: documentation: "https://github.com/brentp/somalier/blob/master/README.md" tool_dev_url: "https://github.com/brentp/somalier" doi: "10.1186/s13073-020-00761-2" - licence: "MIT License" + licence: ["MIT"] input: - meta: type: map @@ -32,14 +32,29 @@ input: - input_index: type: file description: index file of the input data, e.g., bam.bai, cram.crai + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'hg38' ] - fasta: type: file description: The reference fasta file pattern: "*.{fasta,fna,fas,fa}" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'hg38' ] - fai: type: file description: FASTA index file pattern: "*.fai" + - meta4: + type: map + description: | + Groovy Map containing sites information + e.g. [ id:'hg38' ] - sites: type: file description: sites file in VCF format which can be taken from https://github.com/brentp/somalier diff --git a/modules/nf-core/somalier/extract/tests/main.nf.test b/modules/nf-core/somalier/extract/tests/main.nf.test new file mode 100644 index 00000000..dfc7e8a5 --- /dev/null +++ b/modules/nf-core/somalier/extract/tests/main.nf.test @@ -0,0 +1,84 @@ +nextflow_process { + + name "Test Process SOMALIER_EXTRACT" + script "../main.nf" + process "SOMALIER_EXTRACT" + + tag "modules" + tag "modules_nfcore" + tag "somalier" + tag "somalier/extract" + + test("homo_sapiens - [ bam, bai ], fasta, fai, sites") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'delete_me/somalier/sites_chr21.hg38.vcf.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - [ bam, bai ], fasta, fai, sites -stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'delete_me/somalier/sites_chr21.hg38.vcf.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/somalier/extract/tests/main.nf.test.snap b/modules/nf-core/somalier/extract/tests/main.nf.test.snap new file mode 100644 index 00000000..83df72a4 --- /dev/null +++ b/modules/nf-core/somalier/extract/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "homo_sapiens - [ bam, bai ], fasta, fai, sites": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "normal.somalier:md5,21f0b980edd42ddaa8ab964959c1de02" + ] + ], + "1": [ + "versions.yml:md5,df4e49e9520f49a862026da1aa81dde0" + ], + "extract": [ + [ + { + "id": "test", + "single_end": false + }, + "normal.somalier:md5,21f0b980edd42ddaa8ab964959c1de02" + ] + ], + "versions": [ + "versions.yml:md5,df4e49e9520f49a862026da1aa81dde0" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-01T13:25:23.384476049" + }, + "homo_sapiens - [ bam, bai ], fasta, fai, sites -stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.somalier:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,df4e49e9520f49a862026da1aa81dde0" + ], + "extract": [ + [ + { + "id": "test", + "single_end": false + }, + "test.somalier:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,df4e49e9520f49a862026da1aa81dde0" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-01T13:25:35.741711687" + } +} \ No newline at end of file diff --git a/modules/nf-core/somalier/extract/tests/tags.yml b/modules/nf-core/somalier/extract/tests/tags.yml new file mode 100644 index 00000000..836e3524 --- /dev/null +++ b/modules/nf-core/somalier/extract/tests/tags.yml @@ -0,0 +1,2 @@ +somalier/extract: + - "modules/nf-core/somalier/extract/**" diff --git a/modules/nf-core/somalier/relate/environment.yml b/modules/nf-core/somalier/relate/environment.yml deleted file mode 100644 index b8b70f67..00000000 --- a/modules/nf-core/somalier/relate/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: somalier_relate -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::somalier=0.2.15 diff --git a/modules/nf-core/somalier/relate/main.nf b/modules/nf-core/somalier/relate/main.nf deleted file mode 100644 index a8188b64..00000000 --- a/modules/nf-core/somalier/relate/main.nf +++ /dev/null @@ -1,62 +0,0 @@ - -process SOMALIER_RELATE { - tag "$meta.id" - label 'process_low' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/somalier:0.2.15--h37c5b7d_0': - 'biocontainers/somalier:0.2.15--h37c5b7d_0' }" - - input: - tuple val(meta), path(extract), path(ped) - path(sample_groups) - - output: - tuple val(meta), path("*.html"), emit: html - tuple val(meta), path("*.pairs.tsv"), emit: pairs_tsv - tuple val(meta), path("*.samples.tsv"), emit: samples_tsv - tuple val(meta), path("*.ped"), emit: ped - path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def input_list = extract.collect{"$it"}.join(' ') - def prefix = task.ext.prefix ?: "$meta.id" - def sample_groups_command = sample_groups ? "-g $sample_groups" : "" - def ped_command = ped ? "-p $ped" : "" - - """ - somalier relate \\ - -o ${prefix} \\ - ${input_list} \\ - ${args} \\ - ${sample_groups_command} \\ - ${ped_command} - - cut -f1-6 ${prefix}.samples.tsv | sed -e 's/-9/0/' > ${prefix}_somalier.ped - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - somalier: \$(echo \$(somalier 2>&1) | sed 's/^.*somalier version: //; s/Commands:.*\$//') - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "$meta.id" - - """ - touch ${prefix}.html - touch ${prefix}.pairs.tsv - touch ${prefix}.samples.tsv - touch ${prefix}_somalier.ped - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - somalier: \$(echo \$(somalier 2>&1) | sed 's/^.*somalier version: //; s/Commands:.*\$//') - END_VERSIONS - """ -} diff --git a/modules/nf-core/somalier/relate/meta.yml b/modules/nf-core/somalier/relate/meta.yml deleted file mode 100644 index d1d81c87..00000000 --- a/modules/nf-core/somalier/relate/meta.yml +++ /dev/null @@ -1,63 +0,0 @@ -name: "somalier_relate" -description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs -keywords: - - relatedness - - QC - - bam - - cram - - vcf - - gvcf - - ancestry - - identity - - kinship - - informative sites - - family -tools: - - "somalier": - description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" - homepage: "https://github.com/brentp/somalier" - documentation: "https://github.com/brentp/somalier/blob/master/README.md" - tool_dev_url: "https://github.com/brentp/somalier" - doi: "10.1186/s13073-020-00761-2" - licence: "MIT License" -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - extract: - type: file(s) - description: extract file(s) from Somalier extract - pattern: "*.somalier" - - ped: - type: file - description: optional path to a ped or fam file indicating the expected relationships among samples - pattern: "*.{ped,fam}" - - sample_groups: - type: file - description: optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line - pattern: "*.{txt,csv}" -output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - html: - type: file - description: html file - pattern: "*.html" - - pairs_tsv: - type: file - description: tsv file with output stats for pairs of samples - pattern: "*.pairs.tsv" - - samples_tsv: - type: file - description: tsv file with sample-level information - pattern: "*.samples.tsv" -authors: - - "@ashotmarg" - - "@nvnieuwk" -maintainers: - - "@ashotmarg" - - "@nvnieuwk" diff --git a/modules/nf-core/somalier/relate/somalier-relate.diff b/modules/nf-core/somalier/relate/somalier-relate.diff deleted file mode 100644 index 48dc50f3..00000000 --- a/modules/nf-core/somalier/relate/somalier-relate.diff +++ /dev/null @@ -1,30 +0,0 @@ -Changes in module 'nf-core/somalier/relate' ---- modules/nf-core/somalier/relate/main.nf -+++ modules/nf-core/somalier/relate/main.nf -@@ -16,6 +16,7 @@ - tuple val(meta), path("*.html"), emit: html - tuple val(meta), path("*.pairs.tsv"), emit: pairs_tsv - tuple val(meta), path("*.samples.tsv"), emit: samples_tsv -+ tuple val(meta), path("*.ped"), emit: ped - path "versions.yml", emit: versions - - when: -@@ -36,6 +37,8 @@ - ${sample_groups_command} \\ - ${ped_command} - -+ cut -f1-6 ${prefix}.samples.tsv | sed -e 's/-9/0/' > ${prefix}_somalier.ped -+ - cat <<-END_VERSIONS > versions.yml - "${task.process}": - somalier: \$(echo \$(somalier 2>&1) | sed 's/^.*somalier version: //; s/Commands:.*\$//') -@@ -49,6 +52,7 @@ - touch ${prefix}.html - touch ${prefix}.pairs.tsv - touch ${prefix}.samples.tsv -+ touch ${prefix}_somalier.ped - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - -************************************************************ diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml index 4fe40c56..56cc0fb1 100644 --- a/modules/nf-core/tabix/bgzip/environment.yml +++ b/modules/nf-core/tabix/bgzip/environment.yml @@ -5,3 +5,4 @@ channels: - defaults dependencies: - bioconda::tabix=1.11 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf index 7772e9ad..67991c74 100644 --- a/modules/nf-core/tabix/bgzip/main.nf +++ b/modules/nf-core/tabix/bgzip/main.nf @@ -4,8 +4,8 @@ process TABIX_BGZIP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'biocontainers/tabix:1.11--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : + 'biocontainers/htslib:1.20--h5efdd21_2' }" input: tuple val(meta), path(input) @@ -44,7 +44,8 @@ process TABIX_BGZIP { output = in_bgzip ? input.getBaseName() : "${prefix}.${input.getExtension()}.gz" """ - touch ${output} + echo "" | gzip > ${output} + touch ${output}.gzi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config b/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config new file mode 100644 index 00000000..6b6ff55f --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIP { + ext.args = ' -i' + } +} diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test b/modules/nf-core/tabix/bgzip/tests/main.nf.test new file mode 100644 index 00000000..d784aa07 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test @@ -0,0 +1,111 @@ +nextflow_process { + + name "Test Process TABIX_BGZIP" + script "modules/nf-core/tabix/bgzip/main.nf" + process "TABIX_BGZIP" + + tag "modules" + tag "modules_nfcore" + tag "tabix" + tag "tabix/bgzip" + + test("sarscov2_vcf_bgzip_compress") { + when { + process { + """ + input[0] = [ + [ id:'bgzip_test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.output[0][1]).name + ).match("bgzip_test") + } + ) + } + } + + test("homo_genome_bedgz_compress") { + when { + process { + """ + input[0] = [ + [ id:'bedgz_test' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.output[0][1]).name + ).match("bedgz_test") + } + ) + } + } + + test("sarscov2_vcf_bgzip_compress_stub") { + options '-stub' + config "./bgzip_compress.config" + + when { + process { + """ + input[0] = [ + [ id:"test_stub" ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.output[0][1]).name + ).match("test_stub") + } + ) + } + } + + test("sarscov2_vcf_bgzip_compress_gzi") { + config "./bgzip_compress.config" + when { + process { + """ + input[0] = [ + [ id:"gzi_compress_test" ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gzi[0][1]).name + ).match("gzi_compress_test") + } + ) + } + } +} diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap new file mode 100644 index 00000000..0748143f --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap @@ -0,0 +1,218 @@ +{ + "gzi_compress_test": { + "content": [ + "gzi_compress_test.vcf.gz.gzi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:52:29.328146" + }, + "homo_genome_bedgz_compress": { + "content": [ + { + "0": [ + [ + { + "id": "bedgz_test" + }, + "bedgz_test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ], + "gzi": [ + + ], + "output": [ + [ + { + "id": "bedgz_test" + }, + "bedgz_test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:28:34.159992362" + }, + "test_stub": { + "content": [ + "test_stub.vcf.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:52:20.811489" + }, + "sarscov2_vcf_bgzip_compress": { + "content": [ + { + "0": [ + [ + { + "id": "bgzip_test" + }, + "bgzip_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ], + "gzi": [ + + ], + "output": [ + [ + { + "id": "bgzip_test" + }, + "bgzip_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "versions": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:28:22.087769106" + }, + "sarscov2_vcf_bgzip_compress_gzi": { + "content": [ + { + "0": [ + [ + { + "id": "gzi_compress_test" + }, + "gzi_compress_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "1": [ + [ + { + "id": "gzi_compress_test" + }, + "gzi_compress_test.vcf.gz.gzi:md5,26fd00d4e26141cd11561f6e7d4a2ad0" + ] + ], + "2": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ], + "gzi": [ + [ + { + "id": "gzi_compress_test" + }, + "gzi_compress_test.vcf.gz.gzi:md5,26fd00d4e26141cd11561f6e7d4a2ad0" + ] + ], + "output": [ + [ + { + "id": "gzi_compress_test" + }, + "gzi_compress_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "versions": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:28:57.15091665" + }, + "bgzip_test": { + "content": [ + "bgzip_test.vcf.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:52:03.768295" + }, + "bedgz_test": { + "content": [ + "bedgz_test.bed" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:52:12.453855" + }, + "sarscov2_vcf_bgzip_compress_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test_stub" + }, + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test_stub" + }, + "test_stub.vcf.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ], + "gzi": [ + [ + { + "id": "test_stub" + }, + "test_stub.vcf.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "output": [ + [ + { + "id": "test_stub" + }, + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:28:45.219404786" + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/bgzip/tests/tags.yml b/modules/nf-core/tabix/bgzip/tests/tags.yml new file mode 100644 index 00000000..de0eec86 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/tags.yml @@ -0,0 +1,2 @@ +tabix/bgzip: + - "modules/nf-core/tabix/bgzip/**" diff --git a/modules/nf-core/tabix/bgzip/tests/vcf_none.config b/modules/nf-core/tabix/bgzip/tests/vcf_none.config new file mode 100644 index 00000000..f3a3c467 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/vcf_none.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIP { + ext.args = '' + } +} diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml index 028461c9..b9644de9 100644 --- a/modules/nf-core/tabix/bgziptabix/environment.yml +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -5,3 +5,4 @@ channels: - defaults dependencies: - bioconda::tabix=1.11 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index f9482690..05041f49 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -4,8 +4,8 @@ process TABIX_BGZIPTABIX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'biocontainers/tabix:1.11--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : + 'biocontainers/htslib:1.20--h5efdd21_2' }" input: tuple val(meta), path(input) @@ -24,7 +24,7 @@ process TABIX_BGZIPTABIX { def prefix = task.ext.prefix ?: "${meta.id}" """ bgzip --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz - tabix $args2 ${prefix}.${input.getExtension()}.gz + tabix --threads ${task.cpus} $args2 ${prefix}.${input.getExtension()}.gz cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -35,7 +35,7 @@ process TABIX_BGZIPTABIX { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.${input.getExtension()}.gz + echo "" | gzip > ${prefix}.${input.getExtension()}.gz touch ${prefix}.${input.getExtension()}.gz.tbi touch ${prefix}.${input.getExtension()}.gz.csi diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test new file mode 100644 index 00000000..1a84d74f --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test @@ -0,0 +1,94 @@ +nextflow_process { + + name "Test Process TABIX_BGZIPTABIX" + script "modules/nf-core/tabix/bgziptabix/main.nf" + process "TABIX_BGZIPTABIX" + + tag "modules" + tag "modules_nfcore" + tag "tabix" + tag "tabix/bgziptabix" + + test("sarscov2_bed_tbi") { + config "./tabix_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'tbi_test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gz_tbi[0][1]).name + ).match("tbi_test") + } + ) + } + } + + test("sarscov2_bed_csi") { + config "./tabix_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'csi_test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gz_csi[0][1]).name + ).match("csi_test") + } + ) + } + + } + + test("sarscov2_bed_csi_stub") { + config "./tabix_csi.config" + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gz_csi[0][1]).name + ).match("csi_stub") + } + ) + } + + } + +} diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap new file mode 100644 index 00000000..c166ea72 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap @@ -0,0 +1,167 @@ +{ + "sarscov2_bed_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_test" + }, + "tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", + "tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ], + "gz_csi": [ + + ], + "gz_tbi": [ + [ + { + "id": "tbi_test" + }, + "tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", + "tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c" + ] + ], + "versions": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:29:16.053817543" + }, + "sarscov2_bed_csi": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "csi_test" + }, + "csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", + "csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5" + ] + ], + "2": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ], + "gz_csi": [ + [ + { + "id": "csi_test" + }, + "csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", + "csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5" + ] + ], + "gz_tbi": [ + + ], + "versions": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:29:27.667745444" + }, + "csi_test": { + "content": [ + "csi_test.bed.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:51:00.548801" + }, + "csi_stub": { + "content": [ + "test.bed.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:51:09.218454" + }, + "tbi_test": { + "content": [ + "tbi_test.bed.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:50:51.579654" + }, + "sarscov2_bed_csi_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ], + "gz_csi": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gz_tbi": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:29:45.105209991" + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config b/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config new file mode 100644 index 00000000..fb41a314 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIPTABIX { + ext.args2 = '-p vcf --csi' + } +} diff --git a/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config b/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config new file mode 100644 index 00000000..c1915dc4 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIPTABIX { + ext.args2 = '-p vcf' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/bgziptabix/tests/tags.yml b/modules/nf-core/tabix/bgziptabix/tests/tags.yml new file mode 100644 index 00000000..5052b4d7 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/tags.yml @@ -0,0 +1,2 @@ +tabix/bgziptabix: + - "modules/nf-core/tabix/bgziptabix/**" diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 0c9cbb10..4f498244 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,11 +1,9 @@ name: untar - channels: - conda-forge - bioconda - defaults - dependencies: - conda-forge::grep=3.11 - - conda-forge::sed=4.7 + - conda-forge::sed=4.8 - conda-forge::tar=1.34 diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 8a75bb95..9bd8f554 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -4,8 +4,8 @@ process UNTAR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : + 'nf-core/ubuntu:22.04' }" input: tuple val(meta), path(archive) @@ -52,8 +52,29 @@ process UNTAR { stub: prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, "")) """ - mkdir $prefix - touch ${prefix}/file.txt + mkdir ${prefix} + ## Dry-run untaring the archive to get the files and place all in prefix + if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then + for i in `tar -tf ${archive}`; + do + if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]]; + then + touch \${i} + else + mkdir -p \${i} + fi + done + else + for i in `tar -tf ${archive}`; + do + if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]]; + then + touch ${prefix}/\${i} + else + mkdir -p ${prefix}/\${i} + fi + done + fi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test index 2a7c97bf..c957517a 100644 --- a/modules/nf-core/untar/tests/main.nf.test +++ b/modules/nf-core/untar/tests/main.nf.test @@ -6,6 +6,7 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "untar" + test("test_untar") { when { @@ -19,10 +20,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.untar).match("test_untar") }, + { assert snapshot(process.out).match() }, ) } - } test("test_untar_onlyfiles") { @@ -38,10 +38,48 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.untar).match("test_untar_onlyfiles") }, + { assert snapshot(process.out).match() }, ) } + } + + test("test_untar - stub") { + + options "-stub" + when { + process { + """ + input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } } + test("test_untar_onlyfiles - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + } } diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap index 64550292..ceb91b79 100644 --- a/modules/nf-core/untar/tests/main.nf.test.snap +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -1,42 +1,158 @@ { "test_untar_onlyfiles": { "content": [ - [ - [ + { + "0": [ [ - - ], + [ + + ], + [ + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ + [ + [ + + ], + [ + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-10T12:04:28.231047" + }, + "test_untar_onlyfiles - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ [ - "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + [ + + ], + [ + "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] - ] + } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-02-28T11:49:41.320643" + "timestamp": "2024-07-10T12:04:45.773103" + }, + "test_untar - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ + [ + [ + + ], + [ + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-10T12:04:36.777441" }, "test_untar": { "content": [ - [ - [ + { + "0": [ [ - - ], + [ + + ], + [ + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ [ - "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", - "opts.k2d:md5,a033d00cf6759407010b21700938f543", - "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + [ + + ], + [ + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + ] ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] - ] + } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-02-28T11:49:33.795172" + "timestamp": "2024-07-10T12:04:19.377674" } } \ No newline at end of file diff --git a/modules/nf-core/vardictjava/environment.yml b/modules/nf-core/vardictjava/environment.yml index 92d169fd..4e8905e5 100644 --- a/modules/nf-core/vardictjava/environment.yml +++ b/modules/nf-core/vardictjava/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: + - bioconda::htslib=1.20 - bioconda::vardict-java=1.8.3 diff --git a/modules/nf-core/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf index 50d7dfab..6329391c 100644 --- a/modules/nf-core/vardictjava/main.nf +++ b/modules/nf-core/vardictjava/main.nf @@ -4,8 +4,8 @@ process VARDICTJAVA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/vardict-java:1.8.3--hdfd78af_0': - 'biocontainers/vardict-java:1.8.3--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-731b8c4cf44d76e9aa181af565b9eee448d82a8c:edd70e76f3529411a748168f6eb1a61f29702123-0' : + 'biocontainers/mulled-v2-731b8c4cf44d76e9aa181af565b9eee448d82a8c:edd70e76f3529411a748168f6eb1a61f29702123-0' }" input: tuple val(meta), path(bams), path(bais), path(bed) @@ -13,7 +13,7 @@ process VARDICTJAVA { tuple val(meta3), path(fasta_fai) output: - tuple val(meta), path("*.vcf"), emit: vcf + tuple val(meta), path("*.vcf.gz"), emit: vcf path "versions.yml" , emit: versions when: @@ -22,9 +22,10 @@ process VARDICTJAVA { script: def args = task.ext.args ?: '-c 1 -S 2 -E 3' def args2 = task.ext.args2 ?: '' + def args3 = task.ext.args3 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def somatic = bams instanceof ArrayList && bams.size() == 2 ? true : false + def somatic = bams instanceof List && bams.size() == 2 ? true : false def input = somatic ? "-b \"${bams[0]}|${bams[1]}\"" : "-b ${bams}" def filter = somatic ? "testsomatic.R" : "teststrandbias.R" def convert_to_vcf = somatic ? "var2vcf_paired.pl" : "var2vcf_valid.pl" @@ -39,8 +40,7 @@ process VARDICTJAVA { | ${filter} \\ | ${convert_to_vcf} \\ ${args2} \\ - | sed -e 's/##FORMAT= ${prefix}.vcf + | bgzip ${args3} --threads ${task.cpus} > ${prefix}.vcf.gz cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -52,10 +52,11 @@ process VARDICTJAVA { stub: def args = task.ext.args ?: '-c 1 -S 2 -E 3' def args2 = task.ext.args2 ?: '' + def args3 = task.ext.args3 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf + echo '' | gzip > ${prefix}.vcf.gz cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/vardictjava/meta.yml b/modules/nf-core/vardictjava/meta.yml index 657d1531..5c2fc921 100644 --- a/modules/nf-core/vardictjava/meta.yml +++ b/modules/nf-core/vardictjava/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://github.com/AstraZeneca-NGS/VarDictJava" tool_dev_url: "https://github.com/AstraZeneca-NGS/VarDictJava" doi: "10.1093/nar/gkw227 " - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/vardictjava/tests/main.nf.test b/modules/nf-core/vardictjava/tests/main.nf.test index 483a753a..8e5fec10 100644 --- a/modules/nf-core/vardictjava/tests/main.nf.test +++ b/modules/nf-core/vardictjava/tests/main.nf.test @@ -17,17 +17,17 @@ nextflow_process { """ input[0] = Channel.value([ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ]) input[1] = [ [id:"ref"], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [id:"ref"], - file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] """ } @@ -55,22 +55,22 @@ nextflow_process { input[0] = Channel.value([ [ id:'test' ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) ], [ - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai', checkIfExists: true) ], - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ]) input[1] = [ [id:"ref"], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [id:"ref"], - file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] """ } diff --git a/modules/nf-core/vardictjava/tests/main.nf.test.snap b/modules/nf-core/vardictjava/tests/main.nf.test.snap index 4ccb63ec..c32a68b7 100644 --- a/modules/nf-core/vardictjava/tests/main.nf.test.snap +++ b/modules/nf-core/vardictjava/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "test.vcf:md5,e8411ecae49b4f6afa6ea0b681ea506e" + "test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e" ] ], "1": [ @@ -18,7 +18,7 @@ { "id": "test" }, - "test.vcf:md5,e8411ecae49b4f6afa6ea0b681ea506e" + "test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e" ] ], "versions": [ @@ -26,7 +26,11 @@ ] } ], - "timestamp": "2023-10-24T09:24:20.923172332" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-04T19:08:38.328190023" }, "homo_sapiens - [[bam, bam], [bai, bai], bed] - fasta - fai": { "content": [ @@ -36,7 +40,7 @@ { "id": "test" }, - "test.vcf:md5,8acdd8ca041f024aab55d102fb6b0c38" + "test.vcf.gz:md5,b52c874c18be636d876d1e0df4a449c3" ] ], "1": [ @@ -47,7 +51,7 @@ { "id": "test" }, - "test.vcf:md5,8acdd8ca041f024aab55d102fb6b0c38" + "test.vcf.gz:md5,b52c874c18be636d876d1e0df4a449c3" ] ], "versions": [ @@ -55,6 +59,10 @@ ] } ], - "timestamp": "2023-10-24T09:24:29.462707023" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-04T19:08:54.416661915" } } \ No newline at end of file diff --git a/modules/nf-core/vardictjava/vardictjava.diff b/modules/nf-core/vardictjava/vardictjava.diff deleted file mode 100644 index 0efca40b..00000000 --- a/modules/nf-core/vardictjava/vardictjava.diff +++ /dev/null @@ -1,13 +0,0 @@ -Changes in module 'nf-core/vardictjava' ---- modules/nf-core/vardictjava/main.nf -+++ modules/nf-core/vardictjava/main.nf -@@ -39,6 +39,7 @@ - | ${filter} \\ - | ${convert_to_vcf} \\ - ${args2} \\ -+ | sed -e 's/##FORMAT= ${prefix}.vcf - - cat <<-END_VERSIONS > versions.yml - -************************************************************ diff --git a/modules/nf-core/vcf2db/Dockerfile b/modules/nf-core/vcf2db/Dockerfile deleted file mode 100644 index b271f667..00000000 --- a/modules/nf-core/vcf2db/Dockerfile +++ /dev/null @@ -1,11 +0,0 @@ -FROM mambaorg/micromamba:1.4-focal - -COPY ./vcf2db_env.yaml . - -RUN micromamba update --file ./vcf2db_env.yaml --yes -RUN micromamba install --yes --name base --no-deps -c bioconda vcf2db==2020.02.24 -RUN micromamba install --yes --name base --no-deps -c conda-forge coreutils -RUN micromamba clean --all --yes - -ARG MAMBA_DOCKERFILE_ACTIVATE=1 -ENV PATH "$MAMBA_ROOT_PREFIX/bin:$PATH" \ No newline at end of file diff --git a/modules/nf-core/vcf2db/main.nf b/modules/nf-core/vcf2db/main.nf index 85180a37..56c26bb6 100644 --- a/modules/nf-core/vcf2db/main.nf +++ b/modules/nf-core/vcf2db/main.nf @@ -4,7 +4,9 @@ process VCF2DB { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" - container "cmgg/vcf2db:2020.02.24" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/vcf2db:2020.02.24--pl5321hdfd78af_3': + 'biocontainers/vcf2db:2020.02.24--pl5321hdfd78af_3' }" input: tuple val(meta), path(vcf), path(ped) @@ -27,12 +29,6 @@ process VCF2DB { ${prefix}.db \\ $args - sqlite3 ${prefix}.db 'CREATE INDEX idx_variant_impacts_id ON variant_impacts (variant_id)' && \\ - sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN tags varchar(255)' && \\ - sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN tags_user varchar(255)' && \\ - sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN notes varchar(255)' && \\ - sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN notes_user varchar(255)' - cat <<-END_VERSIONS > versions.yml "${task.process}": vcf2db: $VERSION diff --git a/modules/nf-core/vcf2db/tests/main.nf.test b/modules/nf-core/vcf2db/tests/main.nf.test index 52742adf..9532b432 100644 --- a/modules/nf-core/vcf2db/tests/main.nf.test +++ b/modules/nf-core/vcf2db/tests/main.nf.test @@ -15,8 +15,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true) ] """ } @@ -25,7 +25,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + file(process.out.db[0][1]).name, // Conda test fails with content md5 + process.out.versions + ).match() + } ) } @@ -40,8 +44,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true) ] """ } diff --git a/modules/nf-core/vcf2db/tests/main.nf.test.snap b/modules/nf-core/vcf2db/tests/main.nf.test.snap index c51bea34..5e29c6ba 100644 --- a/modules/nf-core/vcf2db/tests/main.nf.test.snap +++ b/modules/nf-core/vcf2db/tests/main.nf.test.snap @@ -28,37 +28,23 @@ ] } ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, "timestamp": "2024-01-10T16:13:32.293507403" }, "homo_sapiens - vcf, ped": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.db:md5,0766bacb306d642a8358b375c4c1836f" - ] - ], - "1": [ - "versions.yml:md5,3d9eedf7998cb77b614736659eb22b1d" - ], - "db": [ - [ - { - "id": "test", - "single_end": false - }, - "test.db:md5,0766bacb306d642a8358b375c4c1836f" - ] - ], - "versions": [ - "versions.yml:md5,3d9eedf7998cb77b614736659eb22b1d" - ] - } + "test.db", + [ + "versions.yml:md5,3d9eedf7998cb77b614736659eb22b1d" + ] ], - "timestamp": "2024-01-10T16:13:25.722991475" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-08-06T10:27:06.932652" } } \ No newline at end of file diff --git a/modules/nf-core/vcf2db/vcf2db_env.yaml b/modules/nf-core/vcf2db/vcf2db_env.yaml deleted file mode 100644 index 1cfa95f8..00000000 --- a/modules/nf-core/vcf2db/vcf2db_env.yaml +++ /dev/null @@ -1,96 +0,0 @@ -name: base -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - _libgcc_mutex=0.1=conda_forge - - _openmp_mutex=4.5=1_llvm - - backports=1.0=py27_1 - - backports.functools_lru_cache=1.6.1=pyhd3eb1b0_0 - - backports.shutil_get_terminal_size=1.0.0=py27_2 - - backports_abc=0.5=py27_0 - - backports.functools_lru_cache=1.6.1=pyhd3eb1b0_0 - - backports_abc=0.5=py27_0 - - blas=2.17=openblas - - bzip2=1.0.8=h516909a_3 - - c-ares=1.17.1=h36c2ea0_0 - - ca-certificates=2020.11.8=ha878542_0 - - certifi=2016.9.26=py27_0 - - click=7.1.2=pyh9f0ad1d_0 - - coloredlogs=14.0=py27h8c360ce_1 - - cycler=0.10.0=py27_0 - - cyvcf2=0.20.9=py27h22a6d1c_0 - - decorator=4.4.2=py_0 - - freetype=2.10.4=he06d7ca_0 - - functools32=3.2.3.2=py27_2 - - futures=3.3.0=py27h8c360ce_1 - - geneimpacts=0.3.7=py27_0 - - htslib=1.10.2=hd3b49d5_1 - - humanfriendly=8.1=py27h8c360ce_1 - - icu=58.2=hf484d3e_1000 - - kiwisolver=1.1.0=py27h9e3301b_1 - - krb5=1.17.2=h926e7f8_0 - - libblas=3.8.0=17_openblas - - libcblas=3.8.0=17_openblas - - libcurl=7.71.1=hcdd3856_8 - - libdeflate=1.6=h516909a_0 - - libedit=3.1.20191231=he28a2e2_2 - - libev=4.33=h516909a_1 - - libffi=3.3=he6710b0_2 - - libgcc-ng=9.3.0=h5dbcf3e_17 - - libgfortran-ng=7.5.0=hae1eefd_17 - - libgfortran4=7.5.0=hae1eefd_17 - - liblapack=3.8.0=17_openblas - - liblapacke=3.8.0=17_openblas - - liblapacke=3.8.0=17_openblas - - libnghttp2=1.41.0=hf8bcb03_2 - - libopenblas=0.3.10=pthreads_hb3c22a3_5 - - libpng=1.6.37=hed695b0_2 - - libssh2=1.9.0=hab1572f_5 - - libstdcxx-ng=9.3.0=h2ae2ef3_17 - - llvm-openmp=11.0.0=hfc4b9b4_1 - - matplotlib-base=2.2.4=py27hfd891ef_0 - - monotonic=1.5=py_0 - - ncurses=6.2=h58526e2_4 - - networkx=2.2=py27_1 - - nomkl=3.0=0 - - numpy=1.16.6=py27h30dfecb_0 - - numpy-base=1.16.6=py27h2f8d375_0 - - numpy-base=1.16.6=py27h2f8d375_0 - - openssl=1.1.1h=h516909a_0 - - pandas=0.24.2=py27hf484d3e_0 - - pathlib2=2.3.5=py27h8c360ce_1 - - patsy=0.5.1=py27_0 - - peddy=0.4.7=pyh864c0ab_0 - - pip=20.1.1=pyh9f0ad1d_0 - - pyparsing=2.4.7=pyh9f0ad1d_0 - - python=2.7.18=h15b4118_1 - - python-dateutil=2.8.1=py_0 - - python-lzo=1.12=py27h42e1302_1001 - - python-snappy=0.5.4=py27hee44bf9_1 - - python_abi=2.7=1_cp27mu - - python-dateutil=2.8.1=py_0 - - python-snappy=0.5.4=py27hee44bf9_1 - - python_abi=2.7=1_cp27mu - - pytz=2020.1=pyh9f0ad1d_0 - - readline=8.0=he28a2e2_2 - - scandir=1.10.0=py27hdf8410d_1 - - scikit-learn=0.20.3=py27ha8026db_1 - - scipy=1.2.1=py27h921218d_2 - - seaborn=0.9.0=py27_0 - - setuptools=44.0.0=py27_0 - - singledispatch=3.4.0.3=py27_1000 - - six=1.15.0=pyh9f0ad1d_0 - - snappy=1.1.8=he1b5a44_3 - - sqlalchemy=1.3.15=py27hdf8410d_1 - - sqlite=3.33.0=h4cf870e_1 - - statsmodels=0.10.2=py27hc1659b7_0 - - subprocess32=3.5.4=py27h516909a_0 - - tk=8.6.10=hed695b0_1 - - toolshed=0.4.6=py27_0 - - tornado=5.1.1=py27h14c3975_1000 - - wheel=0.35.1=pyh9f0ad1d_0 - - xz=5.2.5=h516909a_1 - - zlib=1.2.11=h516909a_1010 - - zstd=1.4.5=h6597ccf_2 diff --git a/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf b/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf index cf7934a4..8c2a2a41 100644 --- a/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf +++ b/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf @@ -134,9 +134,9 @@ workflow GVCF_JOINT_GENOTYPE_GATK4 { GATK4_GENOTYPEGVCFS( ch_genotypegvcfs_input, - ch_fasta.map { meta, fasta -> fasta }, - ch_fai.map { meta, fai -> fai }, - ch_dict.map { meta, dict -> dict }, + ch_fasta, + ch_fai, + ch_dict, ch_dbsnp, ch_dbsnp_tbi ) diff --git a/subworkflows/local/vcf_extract_relate_somalier/main.nf b/subworkflows/local/vcf_extract_relate_somalier/main.nf index 7b09bbfd..d78e4915 100644 --- a/subworkflows/local/vcf_extract_relate_somalier/main.nf +++ b/subworkflows/local/vcf_extract_relate_somalier/main.nf @@ -4,9 +4,9 @@ include { SOMALIER_RELATE } from '../../../modules/nf-core/somalier/relate/main workflow VCF_EXTRACT_RELATE_SOMALIER { take: ch_vcfs // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] - ch_fasta // channel: [mandatory] [ path(fasta) ] - ch_fasta_fai // channel: [mandatory] [ path(fai) ] - ch_somalier_sites // channel: [mandatory] [ path(somalier_sites_vcf) ] + ch_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_fasta_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_somalier_sites // channel: [mandatory] [ val(meta), path(somalier_sites_vcf) ] ch_peds // channel: [mandatory] [ val(meta), path(ped) ] main: diff --git a/workflows/germline.nf b/workflows/germline.nf index 28be6851..b527d130 100644 --- a/workflows/germline.nf +++ b/workflows/germline.nf @@ -136,17 +136,17 @@ workflow GERMLINE { // ch_fasta_ready = Channel.fromPath(fasta).map{ fasta_file -> [[id:"reference"], fasta_file] }.collect() - ch_fai = fai ? Channel.fromPath(fai).map{ fai_file -> [[id:"reference"], fai_file] }.collect() : null - ch_dict = dict ? Channel.fromPath(dict).map{ dict_file -> [[id:"reference"], dict_file] }.collect() : null - ch_strtablefile = strtablefile ? Channel.fromPath(strtablefile).map{ str_file -> [[id:"reference"], str_file] }.collect() : null - ch_sdf = sdf ? Channel.fromPath(sdf).map { sdf_file -> [[id:'reference'], sdf_file] }.collect() : null + ch_fai = fai ? Channel.fromPath(fai).map{ fai_file -> [[id:"reference"], fai_file] }.collect() : null + ch_dict = dict ? Channel.fromPath(dict).map{ dict_file -> [[id:"reference"], dict_file] }.collect() : null + ch_strtablefile = strtablefile ? Channel.fromPath(strtablefile).map{ str_file -> [[id:"reference"], str_file] }.collect() : null + ch_sdf = sdf ? Channel.fromPath(sdf).map { sdf_file -> [[id:'reference'], sdf_file] }.collect() : null ch_default_roi = roi ? Channel.fromPath(roi).collect() : [] - ch_dbsnp_ready = dbsnp ? Channel.fromPath(dbsnp).collect() : [] - ch_dbsnp_tbi = dbsnp_tbi ? Channel.fromPath(dbsnp_tbi).collect() : [] + ch_dbsnp_ready = dbsnp ? Channel.fromPath(dbsnp).collect { dbsnp_file -> [[id:"dbsnp"], dbsnp_file] } : [[],[]] + ch_dbsnp_tbi = dbsnp_tbi ? Channel.fromPath(dbsnp_tbi).collect { dbsnp_file -> [[id:"dbsnp"], dbsnp_file] } : [[],[]] - ch_somalier_sites = somalier_sites ? Channel.fromPath(somalier_sites).collect() : [] + ch_somalier_sites = somalier_sites ? Channel.fromPath(somalier_sites).collect { sites_file -> [[id:"somalier_sites"], sites_file] } : [[],[]] ch_vep_cache = vep_cache ? Channel.fromPath(vep_cache).collect() : [] @@ -518,8 +518,8 @@ workflow GERMLINE { VCF_EXTRACT_RELATE_SOMALIER( ch_normalized_variants, - ch_fasta_ready.map { meta, fasta_file -> fasta_file }, - ch_fai_ready.map { meta, fai_file -> fai_file }, + ch_fasta_ready, + ch_fai_ready, ch_somalier_sites, ch_somalier_input ) From 6d2cdd49f99c5a60c81534be588f66a39cf00ba9 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 4 Sep 2024 17:11:32 +0200 Subject: [PATCH 15/49] pre-commit --- conf/empty.config | 2 +- conf/empty_genomes.config | 2 +- conf/nf_test.config | 2 +- workflows/germline.nf | 10 +++++----- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/conf/empty.config b/conf/empty.config index 11f237e6..19c49241 100644 --- a/conf/empty.config +++ b/conf/empty.config @@ -1 +1 @@ -// DON'T REMOVE THIS FILE \ No newline at end of file +// DON'T REMOVE THIS FILE diff --git a/conf/empty_genomes.config b/conf/empty_genomes.config index e02e8342..a90c75d0 100644 --- a/conf/empty_genomes.config +++ b/conf/empty_genomes.config @@ -1,3 +1,3 @@ // DON'T REMOVE THIS FILE! -params.genomes = [:] \ No newline at end of file +params.genomes = [:] diff --git a/conf/nf_test.config b/conf/nf_test.config index a592580c..3d2c735e 100644 --- a/conf/nf_test.config +++ b/conf/nf_test.config @@ -28,4 +28,4 @@ process { memory: 6.GB, time : 6.h ] -} \ No newline at end of file +} diff --git a/workflows/germline.nf b/workflows/germline.nf index b527d130..a756f7aa 100644 --- a/workflows/germline.nf +++ b/workflows/germline.nf @@ -360,7 +360,7 @@ workflow GERMLINE { ch_input.gvcf .filter { meta, gvcf, tbi -> // Filter out samples that have no GVCF - meta.type == "gvcf" || meta.type == "gvcf_cram" + meta.type == "gvcf" || meta.type == "gvcf_cram" } .branch { meta, gvcf, tbi -> no_tbi: !tbi @@ -385,13 +385,13 @@ workflow GERMLINE { // CRAM_PREPARE_SAMTOOLS_BEDTOOLS( - ch_input.cram.filter { meta, cram, crai -> + ch_input.cram.filter { meta, cram, crai -> // Filter out files that already have a called GVCF when only GVCF callers are used - meta.type == "cram" || (meta.type == "gvcf_cram" && callers - GlobalVariables.gvcfCallers) - }, + meta.type == "cram" || (meta.type == "gvcf_cram" && callers - GlobalVariables.gvcfCallers) + }, ch_input.roi.filter { meta, roi_file -> // Filter out files that already have a called GVCF when only GVCF callers are used - meta.type == "cram" || (meta.type == "gvcf_cram" && callers - GlobalVariables.gvcfCallers) + meta.type == "cram" || (meta.type == "gvcf_cram" && callers - GlobalVariables.gvcfCallers) }, ch_fasta_ready, ch_fai_ready, From 212370b638077ba694464795fc0ed49c347e12f4 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 4 Sep 2024 17:12:05 +0200 Subject: [PATCH 16/49] prettier --- .nf-core.yml | 58 ++++++++++++++++++++++++++-------------------------- 1 file changed, 29 insertions(+), 29 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 7c0e227a..7d44b8c7 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,33 +1,33 @@ lint: - files_exist: - - "CODE_OF_CONDUCT.md" - - "assets/nf-core-germline_logo_light.png" - - "docs/images/nf-core-germline_logo_light.png" - - "docs/images/nf-core-germline_logo_dark.png" - - ".github/ISSUE_TEMPLATE/config.yml" - - ".github/workflows/awstest.yml" - - ".github/workflows/awsfulltest.yml" - - "docs/README.md" - files_unchanged: - - ".github/CONTRIBUTING.md" - - ".github/PULL_REQUEST_TEMPLATE.md" - - ".github/workflows/linting_comment.yml" - - ".github/linting.yml" - - "CODE_OF_CONDUCT.md" - - ".github/ISSUE_TEMPLATE/bug_report.yml" - - ".prettierignore" - nextflow_config: - - "custom_config" # TODO Remove this once the new methods are supported - - "manifest.name" - - "manifest.homePage" - - "params.genomes" - - "validation.help.beforeText" - - "validation.help.afterText" - - "validation.summary.beforeText" - - "validation.summary.afterText" - multiqc_config: - - "report_comment" - actions_ci: false # TODO readd this once the linting doesn't act up + files_exist: + - "CODE_OF_CONDUCT.md" + - "assets/nf-core-germline_logo_light.png" + - "docs/images/nf-core-germline_logo_light.png" + - "docs/images/nf-core-germline_logo_dark.png" + - ".github/ISSUE_TEMPLATE/config.yml" + - ".github/workflows/awstest.yml" + - ".github/workflows/awsfulltest.yml" + - "docs/README.md" + files_unchanged: + - ".github/CONTRIBUTING.md" + - ".github/PULL_REQUEST_TEMPLATE.md" + - ".github/workflows/linting_comment.yml" + - ".github/linting.yml" + - "CODE_OF_CONDUCT.md" + - ".github/ISSUE_TEMPLATE/bug_report.yml" + - ".prettierignore" + nextflow_config: + - "custom_config" # TODO Remove this once the new methods are supported + - "manifest.name" + - "manifest.homePage" + - "params.genomes" + - "validation.help.beforeText" + - "validation.help.afterText" + - "validation.summary.beforeText" + - "validation.summary.afterText" + multiqc_config: + - "report_comment" + actions_ci: false # TODO readd this once the linting doesn't act up nf_core_version: 3.0.0dev repository_type: pipeline template: From 0a81d13fec8f53c34cba7696b06f5f6a6baaebe1 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 4 Sep 2024 17:19:49 +0200 Subject: [PATCH 17/49] fix validate tests --- .../vcf_validate_small_variants/main.nf.test | 13 -------- .../main.nf.test.snap | 33 ++----------------- 2 files changed, 3 insertions(+), 43 deletions(-) diff --git a/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test b/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test index b77bd568..f540a89c 100644 --- a/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test +++ b/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test @@ -45,10 +45,6 @@ nextflow_workflow { input[2] = [[],[]] input[3] = [[],[]] input[4] = UNTAR.out.untar - input[5] = [[],[]] - input[6] = [[],[]] - input[7] = [[],[]] - input[8] = "vcfeval" """ } } @@ -57,15 +53,6 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.happy_vcf, - workflow.out.happy_tbi, - workflow.out.happy_indel_roc, - workflow.out.happy_indel_roc_pass, - workflow.out.happy_snp_roc, - workflow.out.happy_snp_roc_pass, - workflow.out.happy_roc, - workflow.out.happy_summary, - workflow.out.happy_extended_csv, workflow.out.vcfeval_true_positive_vcf, workflow.out.vcfeval_true_positive_vcf_tbi, workflow.out.vcfeval_false_negative_vcf, diff --git a/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test.snap b/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test.snap index 8639b840..3e0b9a14 100644 --- a/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test.snap +++ b/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test.snap @@ -1,33 +1,6 @@ { "default": { "content": [ - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], [ [ { @@ -245,9 +218,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T14:02:50.290466115" + "timestamp": "2024-09-04T17:19:41.712263383" } } \ No newline at end of file From 5b49b84d957286af5c93b3b6cf93d870d574d91b Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 5 Sep 2024 10:14:34 +0200 Subject: [PATCH 18/49] fix somalier tests --- modules.json | 5 + .../nf-core/somalier/relate/environment.yml | 7 + modules/nf-core/somalier/relate/main.nf | 62 ++++ modules/nf-core/somalier/relate/meta.yml | 63 ++++ .../somalier/relate/tests/main.nf.test | 124 ++++++++ .../somalier/relate/tests/main.nf.test.snap | 286 ++++++++++++++++++ .../nf-core/somalier/relate/tests/tags.yml | 2 + .../vcf_extract_relate_somalier/main.nf.test | 12 +- 8 files changed, 555 insertions(+), 6 deletions(-) create mode 100644 modules/nf-core/somalier/relate/environment.yml create mode 100644 modules/nf-core/somalier/relate/main.nf create mode 100644 modules/nf-core/somalier/relate/meta.yml create mode 100644 modules/nf-core/somalier/relate/tests/main.nf.test create mode 100644 modules/nf-core/somalier/relate/tests/main.nf.test.snap create mode 100644 modules/nf-core/somalier/relate/tests/tags.yml diff --git a/modules.json b/modules.json index 16f83c21..af06bdea 100644 --- a/modules.json +++ b/modules.json @@ -171,6 +171,11 @@ "git_sha": "458c882987320e27fc90723ec96c127a243a5497", "installed_by": ["modules"] }, + "somalier/relate": { + "branch": "master", + "git_sha": "458c882987320e27fc90723ec96c127a243a5497", + "installed_by": ["modules"] + }, "tabix/bgzip": { "branch": "master", "git_sha": "b20be35facfc5acdc1259f132ed79339d79e989f", diff --git a/modules/nf-core/somalier/relate/environment.yml b/modules/nf-core/somalier/relate/environment.yml new file mode 100644 index 00000000..5295646b --- /dev/null +++ b/modules/nf-core/somalier/relate/environment.yml @@ -0,0 +1,7 @@ +name: somalier_relate +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::somalier=0.2.19 diff --git a/modules/nf-core/somalier/relate/main.nf b/modules/nf-core/somalier/relate/main.nf new file mode 100644 index 00000000..1c0ba9ae --- /dev/null +++ b/modules/nf-core/somalier/relate/main.nf @@ -0,0 +1,62 @@ + +process SOMALIER_RELATE { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/somalier:0.2.19--h0c29559_0': + 'biocontainers/somalier:0.2.19--h0c29559_0' }" + + input: + tuple val(meta), path(extract), path(ped) + path(sample_groups) + + output: + tuple val(meta), path("*.html"), emit: html + tuple val(meta), path("*.pairs.tsv"), emit: pairs_tsv + tuple val(meta), path("*.samples.tsv"), emit: samples_tsv + tuple val(meta), path("*.ped"), emit: ped + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def input_list = extract.collect{"$it"}.join(' ') + def prefix = task.ext.prefix ?: "$meta.id" + def sample_groups_command = sample_groups ? "-g $sample_groups" : "" + def ped_command = ped ? "-p $ped" : "" + + """ + somalier relate \\ + -o ${prefix} \\ + ${input_list} \\ + ${args} \\ + ${sample_groups_command} \\ + ${ped_command} + + cut -f1-6 ${prefix}.samples.tsv | sed -e 's/-9/0/' > ${prefix}_somalier.ped + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + somalier: \$(echo \$(somalier 2>&1) | sed 's/^.*somalier version: //; s/Commands:.*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "$meta.id" + + """ + touch ${prefix}.html + touch ${prefix}.pairs.tsv + touch ${prefix}.samples.tsv + touch ${prefix}_somalier.ped + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + somalier: \$(echo \$(somalier 2>&1) | sed 's/^.*somalier version: //; s/Commands:.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/somalier/relate/meta.yml b/modules/nf-core/somalier/relate/meta.yml new file mode 100644 index 00000000..42638f4f --- /dev/null +++ b/modules/nf-core/somalier/relate/meta.yml @@ -0,0 +1,63 @@ +name: "somalier_relate" +description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs +keywords: + - relatedness + - QC + - bam + - cram + - vcf + - gvcf + - ancestry + - identity + - kinship + - informative sites + - family +tools: + - "somalier": + description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" + homepage: "https://github.com/brentp/somalier" + documentation: "https://github.com/brentp/somalier/blob/master/README.md" + tool_dev_url: "https://github.com/brentp/somalier" + doi: "10.1186/s13073-020-00761-2" + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - extract: + type: file + description: extract file(s) from Somalier extract + pattern: "*.somalier" + - ped: + type: file + description: optional path to a ped or fam file indicating the expected relationships among samples + pattern: "*.{ped,fam}" + - sample_groups: + type: file + description: optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line + pattern: "*.{txt,csv}" +output: + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - html: + type: file + description: html file + pattern: "*.html" + - pairs_tsv: + type: file + description: tsv file with output stats for pairs of samples + pattern: "*.pairs.tsv" + - samples_tsv: + type: file + description: tsv file with sample-level information + pattern: "*.samples.tsv" +authors: + - "@ashotmarg" + - "@nvnieuwk" +maintainers: + - "@ashotmarg" + - "@nvnieuwk" diff --git a/modules/nf-core/somalier/relate/tests/main.nf.test b/modules/nf-core/somalier/relate/tests/main.nf.test new file mode 100644 index 00000000..5f17456d --- /dev/null +++ b/modules/nf-core/somalier/relate/tests/main.nf.test @@ -0,0 +1,124 @@ +nextflow_process { + + name "Test Process SOMALIER_RELATE" + script "../main.nf" + process "SOMALIER_RELATE" + + tag "modules" + tag "modules_nfcore" + tag "somalier" + tag "somalier/relate" + + test("[ delete_me, [] ], []") { + + when { + process { + """ + input[0] = [ + [ id:'cohort', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'delete_me/somalier/normal.somalier', checkIfExists: true), + file(params.modules_testdata_base_path + 'delete_me/somalier/tumour.somalier', checkIfExists: true) + ], + [] + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("[ delete_me, ped ], groups") { + + when { + process { + """ + input[0] = [ + [ id:'cohort', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'delete_me/somalier/normal.somalier', checkIfExists: true), + file(params.modules_testdata_base_path + 'delete_me/somalier/tumour.somalier', checkIfExists: true) + ], + file(params.modules_testdata_base_path + 'delete_me/somalier/family.ped', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'delete_me/somalier/groups.txt', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("[ delete_me, [] ], [] -stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'cohort', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'delete_me/somalier/normal.somalier', checkIfExists: true), + file(params.modules_testdata_base_path + 'delete_me/somalier/tumour.somalier', checkIfExists: true) + ], + [] + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("[ delete_me, ped ], groups -stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'cohort', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'delete_me/somalier/normal.somalier', checkIfExists: true), + file(params.modules_testdata_base_path + 'delete_me/somalier/tumour.somalier', checkIfExists: true) + ], + file(params.modules_testdata_base_path + 'delete_me/somalier/family.ped', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'delete_me/somalier/groups.txt', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/somalier/relate/tests/main.nf.test.snap b/modules/nf-core/somalier/relate/tests/main.nf.test.snap new file mode 100644 index 00000000..54a73033 --- /dev/null +++ b/modules/nf-core/somalier/relate/tests/main.nf.test.snap @@ -0,0 +1,286 @@ +{ + "[ delete_me, [] ], []": { + "content": [ + { + "0": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.html:md5,03cac9b2c67a8a06f63e07f83ee11e18" + ] + ], + "1": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.pairs.tsv:md5,54d1e9fca1bf9d747d4254c6fa98edcf" + ] + ], + "2": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.samples.tsv:md5,97257d88886db1325c4d7d10cefa7169" + ] + ], + "3": [ + "versions.yml:md5,59d805a9f89558414535c136c814bea6" + ], + "html": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.html:md5,03cac9b2c67a8a06f63e07f83ee11e18" + ] + ], + "pairs_tsv": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.pairs.tsv:md5,54d1e9fca1bf9d747d4254c6fa98edcf" + ] + ], + "samples_tsv": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.samples.tsv:md5,97257d88886db1325c4d7d10cefa7169" + ] + ], + "versions": [ + "versions.yml:md5,59d805a9f89558414535c136c814bea6" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-02T05:29:21.162582556" + }, + "[ delete_me, [] ], [] -stub": { + "content": [ + { + "0": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.pairs.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.samples.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,59d805a9f89558414535c136c814bea6" + ], + "html": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "pairs_tsv": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.pairs.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "samples_tsv": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.samples.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,59d805a9f89558414535c136c814bea6" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-02T05:29:43.887124223" + }, + "[ delete_me, ped ], groups -stub": { + "content": [ + { + "0": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.pairs.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.samples.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,59d805a9f89558414535c136c814bea6" + ], + "html": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "pairs_tsv": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.pairs.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "samples_tsv": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.samples.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,59d805a9f89558414535c136c814bea6" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-02T05:29:55.034913513" + }, + "[ delete_me, ped ], groups": { + "content": [ + { + "0": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.html:md5,0d573016c9279ccdfdcfd4eb01d73b89" + ] + ], + "1": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.pairs.tsv:md5,8655714f1e5359329188e9f501168131" + ] + ], + "2": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.samples.tsv:md5,38ef93340e55fbeef47640abda9e48b0" + ] + ], + "3": [ + "versions.yml:md5,59d805a9f89558414535c136c814bea6" + ], + "html": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.html:md5,0d573016c9279ccdfdcfd4eb01d73b89" + ] + ], + "pairs_tsv": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.pairs.tsv:md5,8655714f1e5359329188e9f501168131" + ] + ], + "samples_tsv": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.samples.tsv:md5,38ef93340e55fbeef47640abda9e48b0" + ] + ], + "versions": [ + "versions.yml:md5,59d805a9f89558414535c136c814bea6" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-02T05:29:32.451456985" + } +} \ No newline at end of file diff --git a/modules/nf-core/somalier/relate/tests/tags.yml b/modules/nf-core/somalier/relate/tests/tags.yml new file mode 100644 index 00000000..c80de730 --- /dev/null +++ b/modules/nf-core/somalier/relate/tests/tags.yml @@ -0,0 +1,2 @@ +somalier/relate: + - "modules/nf-core/somalier/relate/**" diff --git a/tests/subworkflows/local/vcf_extract_relate_somalier/main.nf.test b/tests/subworkflows/local/vcf_extract_relate_somalier/main.nf.test index 09aa4cca..a07570e9 100644 --- a/tests/subworkflows/local/vcf_extract_relate_somalier/main.nf.test +++ b/tests/subworkflows/local/vcf_extract_relate_somalier/main.nf.test @@ -18,9 +18,9 @@ nextflow_workflow { file(params.famvcf, checkIfExists:true), file(params.famtbi, checkIfExists:true) ]) - input[1] = Channel.value(file(params.fasta, checkIfExists:true)) - input[2] = Channel.value(file(params.fai, checkIfExists:true)) - input[3] = Channel.value(file(params.somalier_sites, checkIfExists:true)) + input[1] = Channel.value([[id:"ref"], file(params.fasta, checkIfExists:true)]) + input[2] = Channel.value([[id:"ref"], file(params.fai, checkIfExists:true)]) + input[3] = Channel.value([[id:"ref"], file(params.somalier_sites, checkIfExists:true)]) input[4] = Channel.of([ [id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller"], file(params.ped, checkIfExists:true) @@ -54,9 +54,9 @@ nextflow_workflow { file(params.famvcf, checkIfExists:true), file(params.famtbi, checkIfExists:true) ]) - input[1] = Channel.value(file(params.fasta, checkIfExists:true)) - input[2] = Channel.value(file(params.fai, checkIfExists:true)) - input[3] = Channel.value(file(params.somalier_sites, checkIfExists:true)) + input[1] = Channel.value([[id:"ref"], file(params.fasta, checkIfExists:true)]) + input[2] = Channel.value([[id:"ref"], file(params.fai, checkIfExists:true)]) + input[3] = Channel.value([[id:"ref"], file(params.somalier_sites, checkIfExists:true)]) input[4] = Channel.of([ [id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller"], [] From e33f082d29615f83580e54856d95a31c912115c1 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 5 Sep 2024 10:14:54 +0200 Subject: [PATCH 19/49] fix somalier tests --- modules.json | 184 +++++++++++++----- .../somalier/relate/somalier-relate.diff | 36 ++++ 2 files changed, 174 insertions(+), 46 deletions(-) create mode 100644 modules/nf-core/somalier/relate/somalier-relate.diff diff --git a/modules.json b/modules.json index af06bdea..a684404e 100644 --- a/modules.json +++ b/modules.json @@ -8,208 +8,292 @@ "bcftools/annotate": { "branch": "master", "git_sha": "88ae68490e8f2478a1e1bbeedac970fd7cc73022", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff" }, "bcftools/concat": { "branch": "master", "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "vcf_annotate_ensemblvep_snpeff" + ] }, "bcftools/filter": { "branch": "master", "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/norm": { "branch": "master", "git_sha": "f6cc00f107826cfaf1c933297b10ed1757b41479", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/pluginscatter": { "branch": "master", "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "vcf_annotate_ensemblvep_snpeff" + ] }, "bcftools/query": { "branch": "master", "git_sha": "34ac993e081b32d2170ab790d0386b74122f9d36", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/reheader": { "branch": "master", "git_sha": "c32611ac6813055b9321d2827678e2f8aebcb394", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/sort": { "branch": "master", "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "vcf_annotate_ensemblvep_snpeff" + ] }, "bcftools/stats": { "branch": "master", "git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/intersect": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/merge": { "branch": "master", "git_sha": "a3d614e4a7b8691a259bcfe33ad80903217d6215", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/split": { "branch": "master", "git_sha": "6dc8a32e32158bb4d3f9af92c802233b5d4f8e4d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ensemblvep/download": { "branch": "master", "git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ensemblvep/vep": { "branch": "master", "git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "vcf_annotate_ensemblvep_snpeff" + ] }, "gatk4/calibratedragstrmodel": { "branch": "master", "git_sha": "3f42e07a1133064c569b0dbe182979527bca9e59", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/composestrtablefile": { "branch": "master", "git_sha": "926e2f394d01c71d3abbdbca9c588630bfe51abf", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/createsequencedictionary": { "branch": "master", "git_sha": "e6fe277739f5894711405af3e717b2470bd956b5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/genomicsdbimport": { "branch": "master", "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/genotypegvcfs": { "branch": "master", "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/haplotypecaller": { "branch": "master", "git_sha": "c332ea831f95f750be962c4b5de655f7a1e6e245", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gawk": { "branch": "master", "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "mosdepth": { "branch": "master", "git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "19ca321db5d8bd48923262c2eca6422359633491", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rtgtools/format": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rtgtools/pedfilter": { "branch": "master", "git_sha": "c1c2a770cfb0bfbf093a2434a27f091ebbc65987", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rtgtools/rocplot": { "branch": "master", "git_sha": "64770369d851c45c364e410e052ef9a6c3a7d2bb", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rtgtools/vcfeval": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/convert": { "branch": "master", "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/faidx": { "branch": "master", "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/index": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/merge": { "branch": "master", "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "snpeff/snpeff": { "branch": "master", "git_sha": "3ad7292d9b8da881386e9d5b58364d7da489b38b", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "vcf_annotate_ensemblvep_snpeff" + ] }, "somalier/extract": { "branch": "master", "git_sha": "458c882987320e27fc90723ec96c127a243a5497", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "somalier/relate": { "branch": "master", "git_sha": "458c882987320e27fc90723ec96c127a243a5497", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ], + "patch": "modules/nf-core/somalier/relate/somalier-relate.diff" }, "tabix/bgzip": { "branch": "master", "git_sha": "b20be35facfc5acdc1259f132ed79339d79e989f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/tabix": { "branch": "master", "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", - "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "modules", + "vcf_annotate_ensemblvep_snpeff" + ] }, "untar": { "branch": "master", "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vardictjava": { "branch": "master", "git_sha": "e61e5a13ef49c5595986bd31efb85c3f0709a282", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcf2db": { "branch": "master", "git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcfanno": { "branch": "master", "git_sha": "9a8bba5910982ae637dedb8664e3121db77e173f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -218,25 +302,33 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_annotate_ensemblvep_snpeff": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/somalier/relate/somalier-relate.diff b/modules/nf-core/somalier/relate/somalier-relate.diff new file mode 100644 index 00000000..918d80b2 --- /dev/null +++ b/modules/nf-core/somalier/relate/somalier-relate.diff @@ -0,0 +1,36 @@ +Changes in module 'nf-core/somalier/relate' +Changes in 'somalier/relate/main.nf': +--- modules/nf-core/somalier/relate/main.nf ++++ modules/nf-core/somalier/relate/main.nf +@@ -16,6 +16,7 @@ + tuple val(meta), path("*.html"), emit: html + tuple val(meta), path("*.pairs.tsv"), emit: pairs_tsv + tuple val(meta), path("*.samples.tsv"), emit: samples_tsv ++ tuple val(meta), path("*.ped"), emit: ped + path "versions.yml", emit: versions + + when: +@@ -36,6 +37,8 @@ + ${sample_groups_command} \\ + ${ped_command} + ++ cut -f1-6 ${prefix}.samples.tsv | sed -e 's/-9/0/' > ${prefix}_somalier.ped ++ + cat <<-END_VERSIONS > versions.yml + "${task.process}": + somalier: \$(echo \$(somalier 2>&1) | sed 's/^.*somalier version: //; s/Commands:.*\$//') +@@ -49,6 +52,7 @@ + touch ${prefix}.html + touch ${prefix}.pairs.tsv + touch ${prefix}.samples.tsv ++ touch ${prefix}_somalier.ped + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + +'modules/nf-core/somalier/relate/environment.yml' is unchanged +'modules/nf-core/somalier/relate/meta.yml' is unchanged +'modules/nf-core/somalier/relate/tests/tags.yml' is unchanged +'modules/nf-core/somalier/relate/tests/main.nf.test' is unchanged +'modules/nf-core/somalier/relate/tests/main.nf.test.snap' is unchanged +************************************************************ From f852ed288815eb34c885bfbdce6e30350912fbe6 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 5 Sep 2024 10:42:02 +0200 Subject: [PATCH 20/49] fix rtgtools testz --- modules/nf-core/rtgtools/pedfilter/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/rtgtools/pedfilter/main.nf b/modules/nf-core/rtgtools/pedfilter/main.nf index f6486e17..c06a33fa 100644 --- a/modules/nf-core/rtgtools/pedfilter/main.nf +++ b/modules/nf-core/rtgtools/pedfilter/main.nf @@ -34,6 +34,7 @@ process RTGTOOLS_PEDFILTER { rtg pedfilter \\ ${args} \\ ${input} \\ + | head -n -1 \\ ${postprocess} > ${prefix}.${extension} From b481cb557b54203c65fd488e0b67da88b660f87a Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 5 Sep 2024 10:42:23 +0200 Subject: [PATCH 21/49] fix rtgtools testz --- modules.json | 3 ++- .../pedfilter/rtgtools-pedfilter.diff | 19 +++++++++++++++++++ 2 files changed, 21 insertions(+), 1 deletion(-) create mode 100644 modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff diff --git a/modules.json b/modules.json index a684404e..05ffdf2e 100644 --- a/modules.json +++ b/modules.json @@ -179,7 +179,8 @@ "git_sha": "c1c2a770cfb0bfbf093a2434a27f091ebbc65987", "installed_by": [ "modules" - ] + ], + "patch": "modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff" }, "rtgtools/rocplot": { "branch": "master", diff --git a/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff b/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff new file mode 100644 index 00000000..18590bf8 --- /dev/null +++ b/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff @@ -0,0 +1,19 @@ +Changes in module 'nf-core/rtgtools/pedfilter' +Changes in 'rtgtools/pedfilter/main.nf': +--- modules/nf-core/rtgtools/pedfilter/main.nf ++++ modules/nf-core/rtgtools/pedfilter/main.nf +@@ -34,6 +34,7 @@ + rtg pedfilter \\ + ${args} \\ + ${input} \\ ++ | head -n -1 \\ + ${postprocess} > ${prefix}.${extension} + + + +'modules/nf-core/rtgtools/pedfilter/environment.yml' is unchanged +'modules/nf-core/rtgtools/pedfilter/meta.yml' is unchanged +'modules/nf-core/rtgtools/pedfilter/tests/main.nf.test' is unchanged +'modules/nf-core/rtgtools/pedfilter/tests/main.nf.test.snap' is unchanged +'modules/nf-core/rtgtools/pedfilter/tests/nextflow.config' is unchanged +************************************************************ From 20411ca26176b1a9dfaa22349be0c9f6deaaa948 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 5 Sep 2024 11:27:11 +0200 Subject: [PATCH 22/49] fix more failing tests --- .github/workflows/linting.yml | 3 +- conf/modules.config | 2 +- modules.json | 183 +++++------------- .../local/cram_call_vardictjava/main.nf | 6 +- .../cram_call_genotype_gatk4/main.nf.test | 40 ++-- .../main.nf.test.snap | 40 ++-- 6 files changed, 86 insertions(+), 188 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 7d4ad177..9593436d 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -50,7 +50,8 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + pip install git+https://github.com/nf-core/tools@dev + #pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - name: Run nf-core pipelines lint env: diff --git a/conf/modules.config b/conf/modules.config index f8f93e8f..917f26c0 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -333,7 +333,7 @@ process { } withName: "^.*CRAM_CALL_VARDICTJAVA:VCF_FILTER_BCFTOOLS:FILTER_2\$" { - ext.args = "--soft-filter 'LowFreqBias' --mode '+' -e 'FORMAT/AF[0] < 0.02 && FORMAT/VD[0] < 30 && INFO/SBF < 0.1 && INFO/NM >= 2.0' --output-type z" + ext.args = "--soft-filter 'LowFreqBias' --mode '+' -e 'FORMAT/AF[0:*] < 0.02 && FORMAT/VD[0] < 30 && INFO/SBF < 0.1 && INFO/NM >= 2.0' --output-type z" ext.prefix = enableOutput("filter") ? final_prefix : {"${meta.id}.filtered"} publishDir = [ overwrite: true, diff --git a/modules.json b/modules.json index 05ffdf2e..b4661fa0 100644 --- a/modules.json +++ b/modules.json @@ -8,293 +8,210 @@ "bcftools/annotate": { "branch": "master", "git_sha": "88ae68490e8f2478a1e1bbeedac970fd7cc73022", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff" }, "bcftools/concat": { "branch": "master", "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", - "installed_by": [ - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/filter": { "branch": "master", "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/norm": { "branch": "master", "git_sha": "f6cc00f107826cfaf1c933297b10ed1757b41479", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/pluginscatter": { "branch": "master", "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988", - "installed_by": [ - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/query": { "branch": "master", "git_sha": "34ac993e081b32d2170ab790d0386b74122f9d36", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", "git_sha": "c32611ac6813055b9321d2827678e2f8aebcb394", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", - "installed_by": [ - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/stats": { "branch": "master", "git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/intersect": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/merge": { "branch": "master", "git_sha": "a3d614e4a7b8691a259bcfe33ad80903217d6215", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/split": { "branch": "master", "git_sha": "6dc8a32e32158bb4d3f9af92c802233b5d4f8e4d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ensemblvep/download": { "branch": "master", "git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", "git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0", - "installed_by": [ - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "gatk4/calibratedragstrmodel": { "branch": "master", "git_sha": "3f42e07a1133064c569b0dbe182979527bca9e59", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/composestrtablefile": { "branch": "master", "git_sha": "926e2f394d01c71d3abbdbca9c588630bfe51abf", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", "git_sha": "e6fe277739f5894711405af3e717b2470bd956b5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/genomicsdbimport": { "branch": "master", "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/genotypegvcfs": { "branch": "master", "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/haplotypecaller": { "branch": "master", "git_sha": "c332ea831f95f750be962c4b5de655f7a1e6e245", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gawk": { "branch": "master", "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mosdepth": { "branch": "master", "git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "19ca321db5d8bd48923262c2eca6422359633491", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rtgtools/format": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rtgtools/pedfilter": { "branch": "master", "git_sha": "c1c2a770cfb0bfbf093a2434a27f091ebbc65987", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff" }, "rtgtools/rocplot": { "branch": "master", "git_sha": "64770369d851c45c364e410e052ef9a6c3a7d2bb", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rtgtools/vcfeval": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/convert": { "branch": "master", "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/index": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "snpeff/snpeff": { "branch": "master", "git_sha": "3ad7292d9b8da881386e9d5b58364d7da489b38b", - "installed_by": [ - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "somalier/extract": { "branch": "master", "git_sha": "458c882987320e27fc90723ec96c127a243a5497", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "somalier/relate": { "branch": "master", "git_sha": "458c882987320e27fc90723ec96c127a243a5497", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/somalier/relate/somalier-relate.diff" }, "tabix/bgzip": { "branch": "master", "git_sha": "b20be35facfc5acdc1259f132ed79339d79e989f", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/tabix": { "branch": "master", "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", - "installed_by": [ - "modules", - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff"] }, "untar": { "branch": "master", "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vardictjava": { "branch": "master", "git_sha": "e61e5a13ef49c5595986bd31efb85c3f0709a282", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcf2db": { "branch": "master", "git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcfanno": { "branch": "master", "git_sha": "9a8bba5910982ae637dedb8664e3121db77e173f", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -303,33 +220,25 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_annotate_ensemblvep_snpeff": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} diff --git a/subworkflows/local/cram_call_vardictjava/main.nf b/subworkflows/local/cram_call_vardictjava/main.nf index 0475d947..e7486627 100644 --- a/subworkflows/local/cram_call_vardictjava/main.nf +++ b/subworkflows/local/cram_call_vardictjava/main.nf @@ -1,6 +1,6 @@ include { SAMTOOLS_CONVERT } from '../../../modules/nf-core/samtools/convert/main' include { VARDICTJAVA } from '../../../modules/nf-core/vardictjava/main' -include { TABIX_BGZIPTABIX as TABIX_SPLIT } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { TABIX_TABIX as TABIX_SPLIT } from '../../../modules/nf-core/tabix/tabix/main' include { TABIX_BGZIPTABIX as TABIX_VCFANNO } from '../../../modules/nf-core/tabix/bgziptabix/main' include { BCFTOOLS_REHEADER } from '../../../modules/nf-core/bcftools/reheader/main' include { VCFANNO } from '../../../modules/nf-core/vcfanno/main' @@ -52,7 +52,7 @@ workflow CRAM_CALL_VARDICTJAVA { .set { ch_vardict_crams } ch_cram_bam.bam - .mix(SAMTOOLS_CONVERT.out.alignment_index) + .mix(SAMTOOLS_CONVERT.out.bam.join(SAMTOOLS_CONVERT.out.bai, failOnMismatch:true, failOnDuplicate:true)) .combine(ch_vardict_crams, by:0) .map { meta, bam, bai, cram, crai, bed, split_count -> def new_meta = meta + [id:bed.baseName, split_count:split_count] @@ -73,7 +73,7 @@ workflow CRAM_CALL_VARDICTJAVA { ch_versions = ch_versions.mix(TABIX_SPLIT.out.versions.first()) VCF_CONCAT_BCFTOOLS( - TABIX_SPLIT.out.gz_tbi, + VARDICTJAVA.out.vcf.join(TABIX_SPLIT.out.tbi, failOnMismatch:true, failOnDuplicate:true), false ) ch_versions = ch_versions.mix(VCF_CONCAT_BCFTOOLS.out.versions) diff --git a/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test b/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test index 7ad15931..33425c77 100644 --- a/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test +++ b/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test @@ -53,8 +53,8 @@ nextflow_workflow { [id:"strtablefile"], file(params.strtablefile, checkIfExists:true) ]) - input[6] = [] - input[7] = [] + input[6] = [[],[]] + input[7] = [[],[]] input[8] = false input[9] = false input[10] = false @@ -106,10 +106,8 @@ nextflow_workflow { [id:"strtablefile"], file(params.strtablefile, checkIfExists:true) ]) - input[6] = [] - input[7] = [] - input[6] = [] - input[7] = [] + input[6] = [[],[]] + input[7] = [[],[]] input[8] = false input[9] = false input[10] = false @@ -180,10 +178,8 @@ nextflow_workflow { [id:"strtablefile"], file(params.strtablefile, checkIfExists:true) ]) - input[6] = [] - input[7] = [] - input[6] = [] - input[7] = [] + input[6] = [[],[]] + input[7] = [[],[]] input[8] = false input[9] = false input[10] = false @@ -255,10 +251,8 @@ nextflow_workflow { [id:"strtablefile"], file(params.strtablefile, checkIfExists:true) ]) - input[6] = [] - input[7] = [] - input[6] = [] - input[7] = [] + input[6] = [[],[]] + input[7] = [[],[]] input[8] = false input[9] = false input[10] = false @@ -330,10 +324,8 @@ nextflow_workflow { [id:"strtablefile"], file(params.strtablefile, checkIfExists:true) ]) - input[6] = [] - input[7] = [] - input[6] = [] - input[7] = [] + input[6] = [[],[]] + input[7] = [[],[]] input[8] = false input[9] = true input[10] = false @@ -405,10 +397,8 @@ nextflow_workflow { [id:"strtablefile"], file(params.strtablefile, checkIfExists:true) ]) - input[6] = [] - input[7] = [] - input[6] = [] - input[7] = [] + input[6] = [[],[]] + input[7] = [[],[]] input[8] = false input[9] = false input[10] = true @@ -479,10 +469,8 @@ nextflow_workflow { [id:"strtablefile"], file(params.strtablefile, checkIfExists:true) ]) - input[6] = [] - input[7] = [] - input[6] = [] - input[7] = [] + input[6] = [[],[]] + input[7] = [[],[]] input[8] = false input[9] = false input[10] = false diff --git a/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap b/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap index 64e23b12..6c932f93 100644 --- a/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap +++ b/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap @@ -6,15 +6,15 @@ ], [ [ - "NA24835.haplotypecaller.bcftools_stats.txt:md5,cf8d900f4a7f7844bf1ece4478010459" + "NA24835.haplotypecaller.bcftools_stats.txt:md5,5f42bee02b2bd0d2af2954292ec3b422" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T10:12:27.678293492" + "timestamp": "2024-09-05T11:20:45.005084818" }, "default - family": { "content": [ @@ -33,15 +33,15 @@ ], [ [ - "NA24835.haplotypecaller.bcftools_stats.txt:md5,cf8d900f4a7f7844bf1ece4478010459" + "NA24835.haplotypecaller.bcftools_stats.txt:md5,5f42bee02b2bd0d2af2954292ec3b422" ] ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-06T13:01:36.711373912" + "timestamp": "2024-09-05T11:18:02.353352239" }, "filter - family": { "content": [ @@ -60,15 +60,15 @@ ], [ [ - "NA24835.haplotypecaller.bcftools_stats.txt:md5,cf8d900f4a7f7844bf1ece4478010459" + "NA24835.haplotypecaller.bcftools_stats.txt:md5,5f42bee02b2bd0d2af2954292ec3b422" ] ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-06T13:02:26.651064532" + "timestamp": "2024-09-05T11:19:14.883570897" }, "default - gvcfs": { "content": [ @@ -112,15 +112,15 @@ ], [ [ - "NA24143.haplotypecaller.bcftools_stats.txt:md5,8832acfa6af30e9225b151da201733c3" + "NA24143.haplotypecaller.bcftools_stats.txt:md5,09b4e7674e0f5b98b1e548df3002250e" ] ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-06T12:55:51.608812907" + "timestamp": "2024-09-05T11:16:25.448441115" }, "only_call - family": { "content": [ @@ -129,15 +129,15 @@ ], [ [ - "NA24835.haplotypecaller.bcftools_stats.txt:md5,cf8d900f4a7f7844bf1ece4478010459" + "NA24835.haplotypecaller.bcftools_stats.txt:md5,5f42bee02b2bd0d2af2954292ec3b422" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T10:11:35.142110509" + "timestamp": "2024-09-05T11:20:04.714403906" }, "only_merge - sample + family": { "content": [ @@ -156,14 +156,14 @@ ], [ [ - "NA24835.haplotypecaller.bcftools_stats.txt:md5,cf8d900f4a7f7844bf1ece4478010459" + "NA24835.haplotypecaller.bcftools_stats.txt:md5,5f42bee02b2bd0d2af2954292ec3b422" ] ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-06T13:04:20.473178165" + "timestamp": "2024-09-05T11:21:57.601081087" } } \ No newline at end of file From 2adfe1bab2f492dd6c69728ef3b1602b63967991 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 5 Sep 2024 12:44:54 +0200 Subject: [PATCH 23/49] fix all the things? --- .../local/cram_call_vardictjava/main.nf | 2 +- tests/pipeline/callers/main.nf.test.snap | 38 ++++++---- tests/pipeline/default/main.nf.test.snap | 12 ++-- tests/pipeline/gvcfs/main.nf.test.snap | 9 +-- tests/pipeline/variations/main.nf.test.snap | 71 ++++++++++++------- tests/pipeline/variations2/main.nf.test.snap | 60 ++++++++++------ .../local/cram_call_vardictjava/main.nf.test | 12 ++-- 7 files changed, 133 insertions(+), 71 deletions(-) diff --git a/subworkflows/local/cram_call_vardictjava/main.nf b/subworkflows/local/cram_call_vardictjava/main.nf index e7486627..203bdc7c 100644 --- a/subworkflows/local/cram_call_vardictjava/main.nf +++ b/subworkflows/local/cram_call_vardictjava/main.nf @@ -79,7 +79,7 @@ workflow CRAM_CALL_VARDICTJAVA { ch_versions = ch_versions.mix(VCF_CONCAT_BCFTOOLS.out.versions) ch_dbsnp_annotated = Channel.empty() - if(ch_dbsnp) { + if(ch_dbsnp != [[],[]]) { ch_dbsnp .map { meta, dbsnp -> [ get_vcfanno_config(dbsnp) ] } .collect() diff --git a/tests/pipeline/callers/main.nf.test.snap b/tests/pipeline/callers/main.nf.test.snap index b6f693f0..babe4775 100644 --- a/tests/pipeline/callers/main.nf.test.snap +++ b/tests/pipeline/callers/main.nf.test.snap @@ -2,23 +2,26 @@ "haplotypecaller": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -29,37 +32,41 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:40:41.593827142" + "timestamp": "2024-09-05T11:39:15.537730988" }, "vardict + haplotypecaller": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -70,15 +77,19 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/NA24143.vardict.ped", "test/Ashkenazim/NA24143.vardict.vcf.gz", + "test/Ashkenazim/NA24143.vardict.vcf.gz.csi", "test/Ashkenazim/NA24143.vardict.vcf.gz.tbi", "test/Ashkenazim/NA24149.vardict.ped", "test/Ashkenazim/NA24149.vardict.vcf.gz", + "test/Ashkenazim/NA24149.vardict.vcf.gz.csi", "test/Ashkenazim/NA24149.vardict.vcf.gz.tbi", "test/Ashkenazim/NA24385.vardict.ped", "test/Ashkenazim/NA24385.vardict.vcf.gz", + "test/Ashkenazim/NA24385.vardict.vcf.gz.csi", "test/Ashkenazim/NA24385.vardict.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html", @@ -91,15 +102,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:41:56.768447097" + "timestamp": "2024-09-05T11:56:32.019963111" }, "vardict": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", @@ -116,12 +127,15 @@ "samplesheet.csv", "test/Ashkenazim/NA24143.vardict.ped", "test/Ashkenazim/NA24143.vardict.vcf.gz", + "test/Ashkenazim/NA24143.vardict.vcf.gz.csi", "test/Ashkenazim/NA24143.vardict.vcf.gz.tbi", "test/Ashkenazim/NA24149.vardict.ped", "test/Ashkenazim/NA24149.vardict.vcf.gz", + "test/Ashkenazim/NA24149.vardict.vcf.gz.csi", "test/Ashkenazim/NA24149.vardict.vcf.gz.tbi", "test/Ashkenazim/NA24385.vardict.ped", "test/Ashkenazim/NA24385.vardict.vcf.gz", + "test/Ashkenazim/NA24385.vardict.vcf.gz.csi", "test/Ashkenazim/NA24385.vardict.vcf.gz.tbi", "test/Ashkenazim/reports/NA24143.vardict.bcftools_stats.txt", "test/Ashkenazim/reports/NA24143.vardict.somalier.html", @@ -132,9 +146,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:39:37.704366119" + "timestamp": "2024-09-05T11:54:10.944847435" } } \ No newline at end of file diff --git a/tests/pipeline/default/main.nf.test.snap b/tests/pipeline/default/main.nf.test.snap index 4e35a9bf..30d78cd0 100644 --- a/tests/pipeline/default/main.nf.test.snap +++ b/tests/pipeline/default/main.nf.test.snap @@ -2,23 +2,26 @@ "default": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -29,15 +32,16 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:34:28.414261433" + "timestamp": "2024-09-05T11:40:36.127517277" } } \ No newline at end of file diff --git a/tests/pipeline/gvcfs/main.nf.test.snap b/tests/pipeline/gvcfs/main.nf.test.snap index 430c3e0a..03a3b401 100644 --- a/tests/pipeline/gvcfs/main.nf.test.snap +++ b/tests/pipeline/gvcfs/main.nf.test.snap @@ -2,7 +2,7 @@ "gvcfs": { "content": [ [ - + "[:]" ], [ "multiqc/multiqc_plots", @@ -11,15 +11,16 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T17:18:10.515388658" + "timestamp": "2024-09-05T11:41:32.108980116" } } \ No newline at end of file diff --git a/tests/pipeline/variations/main.nf.test.snap b/tests/pipeline/variations/main.nf.test.snap index 988e32fc..ee31f079 100644 --- a/tests/pipeline/variations/main.nf.test.snap +++ b/tests/pipeline/variations/main.nf.test.snap @@ -2,23 +2,26 @@ "filter": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -29,37 +32,41 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:57:27.216291382" + "timestamp": "2024-09-05T11:45:02.491962487" }, "only_call": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -70,31 +77,34 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:58:10.801784853" + "timestamp": "2024-09-05T11:45:47.266012698" }, "annotate + vcfanno": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -105,37 +115,42 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.gzi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:56:25.391105365" + "timestamp": "2024-09-05T11:43:47.539727235" }, "automap": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -146,6 +161,7 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/automap_haplotypecaller/sample1/sample1.HomRegions.cmgg_bio.tsv", "test/Ashkenazim/automap_haplotypecaller/sample1/sample1.HomRegions.pdf", @@ -164,31 +180,34 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-04-04T16:27:21.116595696" + "timestamp": "2024-09-05T11:47:48.972236882" }, "only_merge": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -200,31 +219,34 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T16:28:12.406463008" + "timestamp": "2024-09-05T11:46:37.403799074" }, "annotate": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -235,15 +257,16 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:47:35.270453118" + "timestamp": "2024-09-05T11:42:39.793880467" } } \ No newline at end of file diff --git a/tests/pipeline/variations2/main.nf.test.snap b/tests/pipeline/variations2/main.nf.test.snap index af8cfcfd..ba145d7e 100644 --- a/tests/pipeline/variations2/main.nf.test.snap +++ b/tests/pipeline/variations2/main.nf.test.snap @@ -2,23 +2,26 @@ "gemini": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -30,37 +33,41 @@ "test/Ashkenazim/Ashkenazim.haplotypecaller.db", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T16:31:52.936259443" + "timestamp": "2024-09-05T11:59:55.764681555" }, "normalize": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -71,37 +78,41 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T17:04:19.112262269" + "timestamp": "2024-09-05T11:57:36.725019238" }, "updio": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -112,37 +123,41 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T16:30:38.464359399" + "timestamp": "2024-09-05T11:58:51.377552309" }, "add_ped": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -153,25 +168,27 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T17:09:21.531982672" + "timestamp": "2024-09-05T12:02:31.850254513" }, "validate": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", @@ -197,6 +214,7 @@ "NA24143/validation/haplotypecaller/NA24143.weighted_roc.tsv.gz", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", @@ -222,6 +240,7 @@ "NA24149/validation/haplotypecaller/NA24149.weighted_roc.tsv.gz", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -251,15 +270,16 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T16:33:15.226868795" + "timestamp": "2024-09-05T12:01:21.850991249" } } \ No newline at end of file diff --git a/tests/subworkflows/local/cram_call_vardictjava/main.nf.test b/tests/subworkflows/local/cram_call_vardictjava/main.nf.test index 6cf959b0..b0914d97 100644 --- a/tests/subworkflows/local/cram_call_vardictjava/main.nf.test +++ b/tests/subworkflows/local/cram_call_vardictjava/main.nf.test @@ -48,8 +48,8 @@ nextflow_workflow { [id:"fai"], file(params.fai, checkIfExists:true) ]) - input[4] = [] - input[5] = [] + input[4] = [[],[]] + input[5] = [[],[]] input[6] = false """ } @@ -105,8 +105,8 @@ nextflow_workflow { [id:"fai"], file(params.fai, checkIfExists:true) ]) - input[4] = [] - input[5] = [] + input[4] = [[],[]] + input[5] = [[],[]] input[6] = true """ } @@ -180,8 +180,8 @@ nextflow_workflow { [id:"fai"], file(params.fai, checkIfExists:true) ]) - input[4] = [] - input[5] = [] + input[4] = [[],[]] + input[5] = [[],[]] input[6] = false """ } From 96300061ba615d2d6c9a7732c9ed799b28d59575 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 5 Sep 2024 12:45:46 +0200 Subject: [PATCH 24/49] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0e59e9f4..50d6471f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## Changes 1. Bumped the minimal support nextflow version to `24.04.0` +2. Bumped all modules to the newest versions +3. The pipeline now also outputs `csi` indices ## Refactors From 1565a9f2ee3c9e35584daccc3d474bee16e8460f Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 5 Sep 2024 13:04:45 +0200 Subject: [PATCH 25/49] fix final test? --- .../local/vcf_annotation/main.nf.test.snap | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/tests/subworkflows/local/vcf_annotation/main.nf.test.snap b/tests/subworkflows/local/vcf_annotation/main.nf.test.snap index fdec0b82..12d0ef2c 100644 --- a/tests/subworkflows/local/vcf_annotation/main.nf.test.snap +++ b/tests/subworkflows/local/vcf_annotation/main.nf.test.snap @@ -13,16 +13,16 @@ ] ], [ - "NA241431_annotated.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", - "NA241432_annotated.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", - "NA241433_annotated.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + "NA241430_annotated_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "NA241431_annotated_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "NA241432_annotated_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-28T09:26:20.34701886" + "timestamp": "2024-09-05T12:53:05.739638954" }, "vcfanno": { "content": [ @@ -38,15 +38,15 @@ ] ], [ - "NA241431_annotated.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", - "NA241432_annotated.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", - "NA241433_annotated.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + "NA241430_annotated_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "NA241431_annotated_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "NA241432_annotated_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-28T09:26:37.223392102" + "timestamp": "2024-09-05T12:53:27.894947052" } } \ No newline at end of file From e6681303f127a6dc782b43b6e8dabe89188d03b7 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 5 Sep 2024 13:10:29 +0200 Subject: [PATCH 26/49] make nf-core happy again --- .nf-core.yml | 2 +- modules.json | 2 +- .../genotypegvcfs/gatk4-genotypegvcfs.diff | 13 - modules/nf-core/gatk4/genotypegvcfs/meta.yml | 29 +- .../gatk4/genotypegvcfs/tests/main.nf.test | 285 ++++++++++++++++++ .../genotypegvcfs/tests/main.nf.test.snap | 191 ++++++++++++ 6 files changed, 505 insertions(+), 17 deletions(-) delete mode 100644 modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff create mode 100644 modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap diff --git a/.nf-core.yml b/.nf-core.yml index 7d44b8c7..d6b21f91 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -12,7 +12,7 @@ lint: - ".github/CONTRIBUTING.md" - ".github/PULL_REQUEST_TEMPLATE.md" - ".github/workflows/linting_comment.yml" - - ".github/linting.yml" + - ".github/workflows/linting.yml" - "CODE_OF_CONDUCT.md" - ".github/ISSUE_TEMPLATE/bug_report.yml" - ".prettierignore" diff --git a/modules.json b/modules.json index b4661fa0..b9a65237 100644 --- a/modules.json +++ b/modules.json @@ -98,7 +98,7 @@ }, "gatk4/genotypegvcfs": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", + "git_sha": "8b74c800af3d91e0d7bfbecb902308dc4369071c", "installed_by": ["modules"] }, "gatk4/haplotypecaller": { diff --git a/modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff b/modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff deleted file mode 100644 index 2369ffbc..00000000 --- a/modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff +++ /dev/null @@ -1,13 +0,0 @@ -Changes in module 'nf-core/gatk4/genotypegvcfs' ---- modules/nf-core/gatk4/genotypegvcfs/main.nf -+++ modules/nf-core/gatk4/genotypegvcfs/main.nf -@@ -1,6 +1,6 @@ - process GATK4_GENOTYPEGVCFS { - tag "$meta.id" -- label 'process_high' -+ label 'process_single' - - conda "bioconda::gatk4=4.4.0.0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - -************************************************************ diff --git a/modules/nf-core/gatk4/genotypegvcfs/meta.yml b/modules/nf-core/gatk4/genotypegvcfs/meta.yml index 8f1e377e..eb704364 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/meta.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/meta.yml @@ -20,10 +20,10 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - gvcf: + - input: type: file description: | - gVCF(.gz) file or to a GenomicsDB + gVCF(.gz) file or a GenomicsDB pattern: "*.{vcf,vcf.gz}" - gvcf_index: type: file @@ -36,22 +36,47 @@ input: - intervals_index: type: file description: Interval index file (optional) + - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] - fasta: type: file description: Reference fasta file pattern: "*.fasta" + - meta3: + type: map + description: | + Groovy Map containing fai information + e.g. [ id:'test' ] - fai: type: file description: Reference fasta index file pattern: "*.fai" + - meta4: + type: map + description: | + Groovy Map containing dict information + e.g. [ id:'test' ] - dict: type: file description: Reference fasta sequence dict file pattern: "*.dict" + - meta5: + type: map + description: | + Groovy Map containing dbsnp information + e.g. [ id:'test' ] - dbsnp: type: file description: dbSNP VCF file pattern: "*.vcf.gz" + - meta6: + type: map + description: | + Groovy Map containing dbsnp tbi information + e.g. [ id:'test' ] - dbsnp_tbi: type: file description: dbSNP VCF index file diff --git a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test new file mode 100644 index 00000000..25bc2d38 --- /dev/null +++ b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test @@ -0,0 +1,285 @@ +nextflow_process { + + name "Test Process GATK4_GENOTYPEGVCFS" + script "../main.nf" + process "GATK4_GENOTYPEGVCFS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/genotypegvcfs" + tag "untar" + + setup { + run("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = [ + [id:"test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz', checkIfExists: true) + ] + """ + } + } + } + + test("homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], []") { + + when { + process { + """ + input[0] = [ + [id:"test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true), + [], + [] + ] + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] }, + process.out.tbi.collect { [it[0], file(it[1]).name] }, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [gvcf_gz, tbi, [], []], fasta, fai, dict, dbsnp, dbsnp_tbi") { + + when { + process { + """ + input[0] = [ + [id:"test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + [], + [] + ] + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [ + [id:"dbsnp"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists:true) + ] + input[5] = [ + [id:"dbsnp"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists:true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] }, + process.out.tbi.collect { [it[0], file(it[1]).name] }, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [gvcf_gz, tbi, bed, []], fasta, fai, dict, [], []") { + + when { + process { + """ + input[0] = [ + [id:"test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists:true), + [] + ] + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] }, + process.out.tbi.collect { [it[0], file(it[1]).name] }, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [gendb, [], [], []], fasta, fai, dict, [], []") { + + when { + process { + """ + input[0] = UNTAR.out.untar.map { meta, gendb -> [ meta, gendb, [], [], []] } + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] }, + process.out.tbi.collect { [it[0], file(it[1]).name] }, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [gendb, bed, [], []], fasta, fai, dict, [], []") { + + when { + process { + """ + input[0] = UNTAR.out.untar.map { meta, gendb -> + [ + meta, + gendb, + [], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists:true), + [] + ] + } + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] }, + process.out.tbi.collect { [it[0], file(it[1]).name] }, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], [] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [id:"test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true), + [], + [] + ] + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap new file mode 100644 index 00000000..1621618e --- /dev/null +++ b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap @@ -0,0 +1,191 @@ +{ + "homo_sapiens - [gendb, [], [], []], fasta, fai, dict, [], []": { + "content": [ + [ + [ + { + "id": "test" + }, + "1ab95fbc5ec55b208f3001572bec54fa" + ] + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T14:27:24.926097884" + }, + "homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], []": { + "content": [ + [ + [ + { + "id": "test" + }, + "1ab95fbc5ec55b208f3001572bec54fa" + ] + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T14:26:24.426228557" + }, + "homo_sapiens - [gvcf_gz, tbi, bed, []], fasta, fai, dict, [], []": { + "content": [ + [ + [ + { + "id": "test" + }, + "1ab95fbc5ec55b208f3001572bec54fa" + ] + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T14:27:04.179308513" + }, + "homo_sapiens - [gvcf_gz, tbi, [], []], fasta, fai, dict, dbsnp, dbsnp_tbi": { + "content": [ + [ + [ + { + "id": "test" + }, + "9b7d476515e07e5486633c42abd86cc" + ] + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T14:26:43.9088684" + }, + "homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], [] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + ], + "tbi": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T14:19:57.615552867" + }, + "homo_sapiens - [gendb, bed, [], []], fasta, fai, dict, [], []": { + "content": [ + [ + [ + { + "id": "test" + }, + "1ab95fbc5ec55b208f3001572bec54fa" + ] + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T14:27:46.189794941" + } +} \ No newline at end of file From 9a0b314ed532dd40bbe82f68fee8a2142ea293ce Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 5 Sep 2024 17:33:09 +0200 Subject: [PATCH 27/49] implement watchpath --- assets/schema_input.json | 68 ++++++-- conf/modules.config | 8 +- main.nf | 3 +- modules/local/automap/automap/main.nf | 2 +- nextflow_schema.json | 6 + .../cram_prepare_samtools_bedtools/main.nf | 15 +- .../local/gvcf_joint_genotype_gatk4/main.nf | 28 +-- .../utils_cmgg_germline_pipeline/main.nf | 46 ++--- subworkflows/local/vcf_upd_updio/main.nf | 6 +- subworkflows/local/watchpath_handling/main.nf | 160 ++++++++++++++++++ 10 files changed, 256 insertions(+), 86 deletions(-) create mode 100644 subworkflows/local/watchpath_handling/main.nf diff --git a/assets/schema_input.json b/assets/schema_input.json index f5de4eec..f1141ae6 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -16,28 +16,64 @@ "meta": ["family"] }, "cram": { - "type": "string", - "pattern": "^\\S+\\.cram$", - "format": "file-path", - "exists": true + "oneOf": [ + { + "type": "string", + "pattern": "^\\S+\\.cram$", + "format": "file-path", + "exists": true + }, + { + "type": "string", + "pattern": "^watch:\\S+\\.cram$", + "format": "file-path" + } + ] }, "crai": { - "type": "string", - "pattern": "^\\S+\\.crai$", - "format": "file-path", - "exists": true + "oneOf": [ + { + "type": "string", + "pattern": "^\\S+\\.cram\\.crai$", + "format": "file-path", + "exists": true + }, + { + "type": "string", + "pattern": "^watch:\\S+\\.cram\\.crai$", + "format": "file-path" + } + ] }, "gvcf": { - "type": "string", - "pattern": "^\\S+vcf(.gz)?$", - "format": "file-path", - "exists": true + "oneOf": [ + { + "type": "string", + "pattern": "^\\S+\\.g\\.vcf(\\.gz)?$", + "format": "file-path", + "exists": true + }, + { + "type": "string", + "pattern": "^watch:\\S+\\.g\\.vcf(\\.gz)?$", + "format": "file-path" + } + ] }, "tbi": { - "type": "string", - "pattern": "^\\S+\\.tbi$", - "format": "file-path", - "exists": true + "oneOf": [ + { + "type": "string", + "pattern": "^\\S+\\.g\\.vcf\\.gz\\.tbi$", + "format": "file-path", + "exists": true + }, + { + "type": "string", + "pattern": "^watch:\\S+\\.g\\.vcf\\.gz\\.tbi?$", + "format": "file-path" + } + ] }, "roi": { "type": "string", diff --git a/conf/modules.config b/conf/modules.config index 917f26c0..f07bb4f2 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -208,19 +208,19 @@ process { } withName: "^.*CRAM_CALL_GENOTYPE_GATK4:GVCF_JOINT_GENOTYPE_GATK4:GATK4_GENOMICSDBIMPORT\$" { - label = { meta.family_count <= 10 ? "process_medium" : "process_high" } + label = { meta.family_samples.tokenize(",").size() <= 10 ? "process_medium" : "process_high" } time = { 16.h * task.attempt } // Lots of parameters are fetched from https://gatk.broadinstitute.org/hc/en-us/articles/360056138571-GenomicsDBImport-usage-and-performance-guidelines ext.args = { [ - meta.family_count >= 100 ? "--batch-size 100" : "", + meta.family_samples.tokenize(",").size() >= 100 ? "--batch-size 100" : "", "--overwrite-existing-genomicsdb-workspace", "--genomicsdb-shared-posixfs-optimizations", "--merge-input-intervals", "--bypass-feature-reader", "--max-num-intervals-to-import-in-parallel ${task.cpus*10}", "--reader-threads ${task.cpus}", - meta.family_count >= 100 ? "--consolidate" : "", + meta.family_samples.tokenize(",").size() >= 100 ? "--consolidate" : "", "--merge-contigs-into-num-partitions 25" ].join(" ") } @@ -565,7 +565,7 @@ process { withName: "^.*VCF_ROH_AUTOMAP:AUTOMAP_AUTOMAP\$" { ext.prefix = {"automap_${meta.caller}"} ext.args = {[ - meta.family_count > 1 ? "--multivcf" : "--id ${meta.samples}", + meta.family_samples.tokenize(",").size() > 1 ? "--multivcf" : "--id ${meta.family_samples}", params.automap_panel_name ? "--panelname ${params.automap_panel_name}" : "" ].findAll { it != "" }.join(" ")} publishDir = [ diff --git a/main.nf b/main.nf index 988afc56..823c6263 100644 --- a/main.nf +++ b/main.nf @@ -208,7 +208,8 @@ workflow { params.input, params.ped, params.genomes, - params.genome + params.genome, + params.watchdir ) // diff --git a/modules/local/automap/automap/main.nf b/modules/local/automap/automap/main.nf index 36072031..b84535a9 100644 --- a/modules/local/automap/automap/main.nf +++ b/modules/local/automap/automap/main.nf @@ -42,7 +42,7 @@ process AUTOMAP_AUTOMAP { def panel_name = args.contains("--panelname") ? args.split("--panelname")[-1].trim().split(" ")[0] : "" prefix = task.ext.prefix ?: "${meta.id}" - def create_outputs = meta.family_count > 1 ? (1..meta.family_count).collect { number -> + def create_outputs = meta.family_samples.tokenize(",").size() > 1 ? (1..meta.family_samples.tokenize(",").size()).collect { number -> def cmd_prefix = "touch ${prefix}/sample${number}" [ "mkdir ${prefix}/sample${number}", diff --git a/nextflow_schema.json b/nextflow_schema.json index 0fc6f59f..31c7b78e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -28,6 +28,12 @@ "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", "fa_icon": "fas fa-folder-open" }, + "watchdir": { + "type": "string", + "format": "directory-path", + "description": "A folder to watch for the creation of files that start with `watch:` in the samplesheet", + "fa_icon": "fas fa-folder-open" + }, "email": { "type": "string", "description": "Email address for completion summary.", diff --git a/subworkflows/local/cram_prepare_samtools_bedtools/main.nf b/subworkflows/local/cram_prepare_samtools_bedtools/main.nf index b4cdbef5..3be4dab3 100644 --- a/subworkflows/local/cram_prepare_samtools_bedtools/main.nf +++ b/subworkflows/local/cram_prepare_samtools_bedtools/main.nf @@ -31,7 +31,10 @@ workflow CRAM_PREPARE_SAMTOOLS_BEDTOOLS { // ch_crams - .groupTuple() // No size needed here because this runs before any process + .map { meta, cram, crai -> + [ groupKey(meta, meta.duplicate_count), cram, crai] + } + .groupTuple() .branch { meta, cram, crai -> multiple: cram.size() > 1 return [meta, cram] @@ -83,7 +86,10 @@ workflow CRAM_PREPARE_SAMTOOLS_BEDTOOLS { // ch_roi - .groupTuple() // A specified size isn't needed here since this runs before any process using ROI files is executed + .map { meta, roi -> + [ groupKey(meta, meta.duplicate_count), roi ] + } + .groupTuple() .branch { meta, roi -> // Determine whether there is an ROI file given to the current sample // It's possible that a sample is given multiple times in the samplesheet, in which @@ -123,7 +129,10 @@ workflow CRAM_PREPARE_SAMTOOLS_BEDTOOLS { ch_versions = ch_versions.mix(MERGE_ROI_PARAMS.out.versions) ch_roi_branch.missing - .groupTuple() // A specified size isn't needed here since this runs before any process using the default ROI file is executed + .map { meta, bed -> + [ groupKey(meta, meta.duplicate_count), bed ] + } + .groupTuple() .combine(MERGE_ROI_PARAMS.out.bed.map { meta, bed -> bed }) .map { meta, missing, default_roi -> [ meta, default_roi ] diff --git a/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf b/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf index 8c2a2a41..c9114b75 100644 --- a/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf +++ b/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf @@ -47,19 +47,10 @@ workflow GVCF_JOINT_GENOTYPE_GATK4 { ch_gvcfs .map { meta, gvcf, tbi -> // Create the family meta - def new_meta = [ - family: meta.family, - id: meta.family, - family_count: meta.family_count, - caller: meta.caller - ] - [ groupKey(new_meta, meta.family_count.toInteger()), gvcf, tbi, meta.sample ] + def new_meta = meta.subMap(["family", "family_samples", "caller"]) + [id:meta.family] + [ groupKey(new_meta, meta.family_samples.tokenize(",").size()), gvcf, tbi ] } .groupTuple() - .map { meta, gvcf, tbi, samples -> - def new_meta = meta + [samples: "${samples.sort(false).join(',')}"] // Having a comma-separated string ensures that joins don't fail - [ new_meta, gvcf, tbi ] - } .combine(GAWK.out.output.map { meta, bed -> bed }) .map { meta, gvcfs, tbis, bed -> [ meta, gvcfs, tbis, bed, [], [] ] @@ -87,19 +78,10 @@ workflow GVCF_JOINT_GENOTYPE_GATK4 { BCFTOOLS_QUERY.out.output .map { meta, bed -> // Create the family meta - def new_meta = [ - family: meta.family, - id: meta.family, - family_count: meta.family_count, - caller: meta.caller - ] - [ groupKey(new_meta, meta.family_count.toInteger()), bed, meta.sample ] + def new_meta = meta.subMap(["family", "family_samples", "caller"]) + [id:meta.family] + [ groupKey(new_meta, meta.family_samples.tokenize(",").size()), bed ] } .groupTuple() - .map { meta, bed, samples -> - def new_meta = meta + [samples: "${samples.sort(false).join(',')}"] // Having a comma-separated string ensures that joins don't fail - [ new_meta, bed ] - } .dump(tag:'merge_beds_input', pretty: true) .set { ch_merge_beds_input } @@ -116,7 +98,7 @@ workflow GVCF_JOINT_GENOTYPE_GATK4 { INPUT_SPLIT_BEDTOOLS( MERGE_BEDS.out.bed.map { meta, bed -> // Multiply the scatter count by the family size to better scatter big families - [meta, bed, (scatter_count * meta.family_count)] + [meta, bed, (scatter_count * meta.family_samples.tokenize(",").size())] }, GATK4_GENOMICSDBIMPORT.out.genomicsdb.map { meta, genomicsdb -> [ meta, genomicsdb, [] ]} ) diff --git a/subworkflows/local/utils_cmgg_germline_pipeline/main.nf b/subworkflows/local/utils_cmgg_germline_pipeline/main.nf index f70e310a..6124181e 100644 --- a/subworkflows/local/utils_cmgg_germline_pipeline/main.nf +++ b/subworkflows/local/utils_cmgg_germline_pipeline/main.nf @@ -10,12 +10,12 @@ include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' include { paramsSummaryMap } from 'plugin/nf-schema' -include { samplesheetToList } from 'plugin/nf-schema' include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' +include { WATCHPATH_HANDLING } from '../watchpath_handling' /* ======================================================================================== @@ -36,6 +36,7 @@ workflow PIPELINE_INITIALISATION { pedFile // string: Path to the common PED file genomesMap // map: A map structure containing the references for each genome genome // string: The genome to use + watchdir // string: The path to watch for input files main: @@ -75,43 +76,18 @@ workflow PIPELINE_INITIALISATION { // Create channel from input file provided through params.input // - // Output the samplesheet - def input_file = file(input) - input_file.copyTo("${outdir}/samplesheet.csv") - - def pedigree = new Pedigree(pedFile) + WATCHPATH_HANDLING( + input, + watchdir, + "assets/schema_input.json", + pedFile + ) - def samplesheetList = samplesheetToList(input_file, "assets/schema_input.json") - samplesheetList.each { row -> - def ped = row[6] - if(ped) { pedigree.addPedContent(ped) } - } - GlobalVariables.pedFiles = pedigree.writePeds(workflow) - - Channel.fromList(samplesheetList) - .map { meta, cram, crai, gvcf, tbi, roi, ped, truth_vcf, truth_tbi, truth_bed -> - // Infer the family ID from the PED file if no family ID was given. - // If no PED is given, use the sample ID as family ID - def new_meta = meta + [ - family: meta.family ?: pedigree.getFamily(meta.sample) - ] - [ new_meta, cram, crai, gvcf, tbi, roi, truth_vcf, truth_tbi, truth_bed ] - } - .tap { ch_raw_inputs } - .map { row -> - [ "id":row[0].id, "family":row[0].family ] - } - .reduce([:]) { families, v -> - // Count the unique samples in one family - families[v.family] = families[v.family] ? families[v.family] + [v.id] : [v.id] - families[v.family] = families[v.family].unique() - families - } - .combine(ch_raw_inputs) - .set { ch_samplesheet } + // Output the samplesheet + file(input).copyTo("${outdir}/samplesheet.csv") emit: - samplesheet = ch_samplesheet + samplesheet = WATCHPATH_HANDLING.out.samplesheet versions = ch_versions } diff --git a/subworkflows/local/vcf_upd_updio/main.nf b/subworkflows/local/vcf_upd_updio/main.nf index 7cfd7db4..c7c96d2a 100644 --- a/subworkflows/local/vcf_upd_updio/main.nf +++ b/subworkflows/local/vcf_upd_updio/main.nf @@ -17,13 +17,13 @@ workflow VCF_UPD_UPDIO { // Filter out all families that have less than 3 samples ch_vcfs .filter { meta, vcf, tbi -> - meta.family_count >= 3 + meta.family_samples.tokenize(",").size() >= 3 } .set { ch_trio_vcfs } ch_peds .filter { meta, ped -> - meta.family_count >= 3 + meta.family_samples.tokenize(",").size() >= 3 } .set { ch_trio_peds } @@ -31,7 +31,7 @@ workflow VCF_UPD_UPDIO { [failOnDuplicate:true, failOnMismatch:true], ch_trio_vcfs, ch_trio_peds, - ["id", "family", "family_count", "caller"] + ["id", "family", "family_samples", "caller"] ) .map { meta, vcf, tbi, ped -> def meta_list = get_family_data_from_ped(meta, ped) diff --git a/subworkflows/local/watchpath_handling/main.nf b/subworkflows/local/watchpath_handling/main.nf new file mode 100644 index 00000000..ddbda33f --- /dev/null +++ b/subworkflows/local/watchpath_handling/main.nf @@ -0,0 +1,160 @@ +include { samplesheetToList } from 'plugin/nf-schema' + +workflow WATCHPATH_HANDLING { + + take: + input_samplesheet + watchdir + samplesheet_schema + pedFile + + main: + + // A map with entries for every row that expects to be watched + def watch_lines = [:] + + // Initialize a filename for the DONE file + def watch_id = UUID.randomUUID().toString() + def done_file = file("${watchdir}/DONE-${watch_id}") + + // A list containing all expected files + def expected_files = [done_file.name] + + // Initialize samplesheet to keep the linter happy + ch_samplesheet_watched = Channel.empty() + + // Pedigree handling + def pedigree = new Pedigree(pedFile) + GlobalVariables.pedFiles = pedigree.writePeds(workflow) + + def families = [:] + def sample_counts = [:] + + // Determine which files to watch for + def samplesheet_list = samplesheetToList(input_samplesheet, samplesheet_schema) + // Do some calculations and manipulations here + .collect { row -> + // Watchpath logic + def is_watch = false + row = row.collect { input -> + input_name = input instanceof Path ? input.name : input as String + if (input_name.startsWith("watch:")) { + is_watch = true + expected_files.add(input_name.replace("watch:", "")) + return input_name + } + return input + } + if (is_watch) { + watch_lines[row[0].id] = row + } + + // Pipeline logic + def ped = row[6] + if (ped) { + pedigree.addPedContent(ped) + } + def family = row[0].family ?: pedigree.getFamily(row[0].sample) + + if (!families.containsKey(family)) { + families[family] = [row[0].id] + } else { + families[family].add(row[0].id) + } + + if (!sample_counts.containsKey(row[0].id)) { + sample_counts[row[0].id] = 1 + } else { + sample_counts[row[0].id] += 1 + } + + def new_meta = row[0] + [family:family] + row[0] = new_meta + row.remove(6) + return row + } + + println(sample_counts) + + Channel.fromList(samplesheet_list).set { ch_samplesheet_all } + + if (watchdir) { + + watchdir_path = file(watchdir) + if (!watchdir_path.exists()) { + // Create the watchdir if it doesn't exist (this is a failsafe) + watchdir_path.mkdir() + } + + // Watch the watchdir for the expected files + Channel.watchPath("${watchdir}**{${expected_files.join(',')}}", "create,modify") + .until { file -> + def file_name = file.name + if (file_name == done_file.name) { + // Delete the done file when it's been detected and stop watching + done_file.delete() + return true + } + return false + } + .map { file -> + // Try to find a matching ID in watch_lines + def id = find_id(file.name, watch_lines) + if (id == "") { + error("Could not find id for file '${file.name}' in the samplesheet.") + } + // Replace the matching watch entry with the file + watch_lines[id] = watch_lines[id].collect { line_entry -> + line_entry == "watch:${file.name}" as String ? file : line_entry + } + return watch_lines[id] + } + .filter { entry -> + def found_all_files = false + if (!entry.any { elem -> elem.toString().startsWith("watch:") }) { + // Remove the entry from watch_files when all files for the current entry have been found + watch_lines.remove(entry[0].id) + found_all_files = true + } + if (watch_lines.size() == 0) { + // Create the DONE file when all files have been found + done_file.text = "" + } + // Pass through all entries where all files have been found + return found_all_files + } + // Mix with all entries that didn't contain any watched files + .mix(ch_samplesheet_all.filter { entry -> !entry.any { elem -> elem.toString().startsWith("watch:") }}) + .set { ch_samplesheet_watched } + + } else { + ch_samplesheet_watched = ch_samplesheet_all + } + + ch_samplesheet_watched + .map { row -> + row[0] = row[0] + [ + family_samples:families[row[0].family].sort(false).join(","), + duplicate_count:sample_counts[row[0].id] + ] + return row + } + .set { samplesheet } + + emit: + samplesheet + +} + +// Find the ID of a file in a map with sample IDs as keys +def find_id(file_name, file_map) { + def lastDotIndex = file_name.lastIndexOf(".") + if (lastDotIndex == -1) { + return "" + } + def id = file_name.substring(0, lastDotIndex) + if (file_map.containsKey(id)) { + return id + } + return find_id(id, file_map) +} From 722e4eb5731d4e3cb9067e8b516c2a3c28c6506f Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 6 Sep 2024 13:37:17 +0200 Subject: [PATCH 28/49] fix some more issues found with the new import --- subworkflows/local/watchpath_handling/main.nf | 26 +++++++++++++------ workflows/germline.nf | 20 +++++++------- 2 files changed, 27 insertions(+), 19 deletions(-) diff --git a/subworkflows/local/watchpath_handling/main.nf b/subworkflows/local/watchpath_handling/main.nf index ddbda33f..5e96ec58 100644 --- a/subworkflows/local/watchpath_handling/main.nf +++ b/subworkflows/local/watchpath_handling/main.nf @@ -27,6 +27,8 @@ workflow WATCHPATH_HANDLING { def pedigree = new Pedigree(pedFile) GlobalVariables.pedFiles = pedigree.writePeds(workflow) + def errors = [] + def families = [:] def sample_counts = [:] @@ -47,6 +49,9 @@ workflow WATCHPATH_HANDLING { } if (is_watch) { watch_lines[row[0].id] = row + if (!watchdir) { + errors.add("Found a `watch:` prefix in the samplesheet for '${row[0].id}', but no watch directory has been set.") + } } // Pipeline logic @@ -55,17 +60,19 @@ workflow WATCHPATH_HANDLING { pedigree.addPedContent(ped) } def family = row[0].family ?: pedigree.getFamily(row[0].sample) + def sample_id = row[0].id if (!families.containsKey(family)) { - families[family] = [row[0].id] - } else { - families[family].add(row[0].id) + families[family] = [sample_id] + } else if(!families[family].contains(sample_id)) { + families[family].add(sample_id) } - if (!sample_counts.containsKey(row[0].id)) { - sample_counts[row[0].id] = 1 + + if (!sample_counts.containsKey(sample_id)) { + sample_counts[sample_id] = 1 } else { - sample_counts[row[0].id] += 1 + sample_counts[sample_id] += 1 } def new_meta = row[0] + [family:family] @@ -74,7 +81,9 @@ workflow WATCHPATH_HANDLING { return row } - println(sample_counts) + if (errors.size() > 0) { + error(errors.join("\n")) + } Channel.fromList(samplesheet_list).set { ch_samplesheet_all } @@ -129,6 +138,7 @@ workflow WATCHPATH_HANDLING { } else { ch_samplesheet_watched = ch_samplesheet_all + } ch_samplesheet_watched @@ -138,7 +148,7 @@ workflow WATCHPATH_HANDLING { duplicate_count:sample_counts[row[0].id] ] return row - } + }.view() .set { samplesheet } emit: diff --git a/workflows/germline.nf b/workflows/germline.nf index a756f7aa..ec5987a7 100644 --- a/workflows/germline.nf +++ b/workflows/germline.nf @@ -330,24 +330,19 @@ workflow GERMLINE { // ch_samplesheet - .multiMap { families, meta, cram, crai, gvcf, tbi, roi_file, truth_vcf, truth_tbi, truth_bed -> + .multiMap { meta, cram, crai, gvcf, tbi, roi_file, truth_vcf, truth_tbi, truth_bed -> // Divide the input files into their corresponding channel def new_meta = meta + [ - family_count: families[meta.family].size(), // Contains the amount of samples in the family from this sample type: gvcf && cram ? "gvcf_cram" : gvcf ? "gvcf" : "cram" // Define the type of input data ] - def new_meta_validation = [ - id: meta.id, - sample: meta.sample, - family: meta.family - ] + def new_meta_validation = meta.subMap(["id", "sample", "family", "duplicate_count"]) truth_variants: [new_meta_validation, truth_vcf, truth_tbi, truth_bed] // Optional channel containing the truth VCF, its index and the optional BED file gvcf: [new_meta, gvcf, tbi] // Optional channel containing the GVCFs and their optional indices cram: [new_meta, cram, crai] // Mandatory channel containing the CRAM files and their optional indices roi: [new_meta, roi_file] // Optional channel containing the ROI BED files for WES samples - family_samples: [meta.family, families[meta.family]] // A channel containing the samples per family + family_samples: [meta.family, meta.family_samples.tokenize(",")] // A channel containing the samples per family } .set { ch_input } @@ -599,7 +594,10 @@ workflow GERMLINE { if (validate){ ch_input.truth_variants - .groupTuple() // No size needed here since it's being run before any process + .map { meta, vcf, tbi, bed -> + [ groupKey(meta, meta.duplicate_count), vcf, tbi, bed ] + } + .groupTuple() .map { meta, vcf, tbi, bed -> // Get only one VCF for samples that were given multiple times one_vcf = vcf.find { vcf_file -> vcf_file != [] } ?: [] @@ -638,7 +636,7 @@ workflow GERMLINE { ch_final_vcfs .map { meta, vcf, tbi -> - def new_meta = meta - meta.subMap("family_count") + def new_meta = meta - meta.subMap("family_samples") [ meta.family, new_meta, vcf, tbi ] } .combine(ch_family_samples, by:0) @@ -685,7 +683,7 @@ workflow GERMLINE { CustomChannelOperators.joinOnKeys( ch_final_vcfs.map { meta, vcf, tbi -> [ meta, vcf ]}, VCF_EXTRACT_RELATE_SOMALIER.out.peds, - ['id', 'family', 'family_count'] + ['id', 'family', 'family_samples'] ) .dump(tag:'vcf2db_input', pretty:true) .set { ch_vcf2db_input } From 6c88b6f4f6618ce68c42a13b410befbc822d99dd Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 10 Sep 2024 12:39:50 +0200 Subject: [PATCH 29/49] Fix haplotyper resource usage (#192) * Fix haplotyper resource usage --- conf/empty.config | 2 +- conf/empty_genomes.config | 2 +- conf/nf_test.config | 2 +- .../haplotypecaller/gatk4-haplotypecaller.diff | 14 ++++++++++++++ modules/nf-core/gatk4/haplotypecaller/main.nf | 2 +- workflows/germline.nf | 10 +++++----- 6 files changed, 23 insertions(+), 9 deletions(-) diff --git a/conf/empty.config b/conf/empty.config index 11f237e6..19c49241 100644 --- a/conf/empty.config +++ b/conf/empty.config @@ -1 +1 @@ -// DON'T REMOVE THIS FILE \ No newline at end of file +// DON'T REMOVE THIS FILE diff --git a/conf/empty_genomes.config b/conf/empty_genomes.config index e02e8342..a90c75d0 100644 --- a/conf/empty_genomes.config +++ b/conf/empty_genomes.config @@ -1,3 +1,3 @@ // DON'T REMOVE THIS FILE! -params.genomes = [:] \ No newline at end of file +params.genomes = [:] diff --git a/conf/nf_test.config b/conf/nf_test.config index a592580c..3d2c735e 100644 --- a/conf/nf_test.config +++ b/conf/nf_test.config @@ -28,4 +28,4 @@ process { memory: 6.GB, time : 6.h ] -} \ No newline at end of file +} diff --git a/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff b/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff index 275b0dd0..72ac552e 100644 --- a/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff +++ b/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff @@ -1,6 +1,17 @@ Changes in module 'nf-core/gatk4/haplotypecaller' +'modules/nf-core/gatk4/haplotypecaller/environment.yml' is unchanged +'modules/nf-core/gatk4/haplotypecaller/meta.yml' is unchanged +Changes in 'gatk4/haplotypecaller/main.nf': --- modules/nf-core/gatk4/haplotypecaller/main.nf +++ modules/nf-core/gatk4/haplotypecaller/main.nf +@@ -1,6 +1,6 @@ + process GATK4_HAPLOTYPECALLER { + tag "$meta.id" +- label 'process_medium' ++ label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? @@ -12,8 +12,8 @@ tuple val(meta2), path(fasta) tuple val(meta3), path(fai) @@ -13,4 +24,7 @@ Changes in module 'nf-core/gatk4/haplotypecaller' output: tuple val(meta), path("*.vcf.gz") , emit: vcf +'modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap' is unchanged +'modules/nf-core/gatk4/haplotypecaller/tests/tags.yml' is unchanged +'modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test' is unchanged ************************************************************ diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 7170169f..455aedbf 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -1,6 +1,6 @@ process GATK4_HAPLOTYPECALLER { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/workflows/germline.nf b/workflows/germline.nf index 7b51d93a..6fe460dc 100644 --- a/workflows/germline.nf +++ b/workflows/germline.nf @@ -360,7 +360,7 @@ workflow GERMLINE { ch_input.gvcf .filter { meta, gvcf, tbi -> // Filter out samples that have no GVCF - meta.type == "gvcf" || meta.type == "gvcf_cram" + meta.type == "gvcf" || meta.type == "gvcf_cram" } .branch { meta, gvcf, tbi -> no_tbi: !tbi @@ -385,13 +385,13 @@ workflow GERMLINE { // CRAM_PREPARE_SAMTOOLS_BEDTOOLS( - ch_input.cram.filter { meta, cram, crai -> + ch_input.cram.filter { meta, cram, crai -> // Filter out files that already have a called GVCF when only GVCF callers are used - meta.type == "cram" || (meta.type == "gvcf_cram" && callers - GlobalVariables.gvcfCallers) - }, + meta.type == "cram" || (meta.type == "gvcf_cram" && callers - GlobalVariables.gvcfCallers) + }, ch_input.roi.filter { meta, roi_file -> // Filter out files that already have a called GVCF when only GVCF callers are used - meta.type == "cram" || (meta.type == "gvcf_cram" && callers - GlobalVariables.gvcfCallers) + meta.type == "cram" || (meta.type == "gvcf_cram" && callers - GlobalVariables.gvcfCallers) }, ch_fasta_ready, ch_fai_ready, From 2fc05a5dfc9f073793ba02bf24f2fdb7611df5a4 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Tue, 10 Sep 2024 13:23:12 +0200 Subject: [PATCH 30/49] reintroduce nf-core lint support + update all modules (#190) * first steps * resolve all non module linting issues * update all modules * pre-commit * prettier * fix validate tests * fix somalier tests * fix somalier tests * fix rtgtools testz * fix rtgtools testz * fix more failing tests * fix all the things? * update changelog * fix final test? * make nf-core happy again * Fix haplotyper resource usage (#192) * Fix haplotyper resource usage * update all modules --------- Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> --- .github/workflows/linting.yml | 13 +- .github/workflows/linting_comment.yml | 2 +- .nf-core.yml | 44 +- CHANGELOG.md | 2 + CITATIONS.md | 1 + README.md | 2 +- conf/modules.config | 2 +- conf/test_full.config | 4 +- main.nf | 2 +- modules.json | 109 ++- .../bcftools/annotate/bcftools-annotate.diff | 26 + .../nf-core/bcftools/annotate/environment.yml | 2 +- modules/nf-core/bcftools/annotate/main.nf | 20 +- modules/nf-core/bcftools/annotate/meta.yml | 16 +- .../bcftools/annotate/tests/bcf.config | 4 + .../bcftools/annotate/tests/main.nf.test | 327 ++++++++ .../bcftools/annotate/tests/main.nf.test.snap | 388 +++++++++ .../nf-core/bcftools/annotate/tests/tags.yml | 2 + .../bcftools/annotate/tests/vcf.config | 4 + .../annotate/tests/vcf_gz_index.config | 4 + .../annotate/tests/vcf_gz_index_csi.config | 4 + .../annotate/tests/vcf_gz_index_tbi.config | 4 + .../bcftools/concat/bcftools-concat.diff | 40 - .../nf-core/bcftools/concat/environment.yml | 2 +- modules/nf-core/bcftools/concat/main.nf | 31 +- modules/nf-core/bcftools/concat/meta.yml | 8 + .../bcftools/concat/tests/main.nf.test | 254 +++++- .../bcftools/concat/tests/main.nf.test.snap | 370 ++++++++- .../bcftools/concat/tests/vcf_gz_index.config | 4 + .../concat/tests/vcf_gz_index_csi.config | 4 + .../concat/tests/vcf_gz_index_tbi.config | 4 + .../nf-core/bcftools/filter/environment.yml | 2 +- modules/nf-core/bcftools/filter/main.nf | 18 +- modules/nf-core/bcftools/filter/meta.yml | 8 + .../bcftools/filter/tests/main.nf.test | 177 +++- .../bcftools/filter/tests/main.nf.test.snap | 318 +++++++- .../bcftools/filter/tests/vcf_gz_index.config | 4 + .../filter/tests/vcf_gz_index_csi.config | 4 + .../filter/tests/vcf_gz_index_tbi.config | 4 + modules/nf-core/bcftools/norm/environment.yml | 2 +- modules/nf-core/bcftools/norm/main.nf | 22 +- modules/nf-core/bcftools/norm/meta.yml | 8 + .../nf-core/bcftools/norm/tests/main.nf.test | 563 +++++++++++++ .../bcftools/norm/tests/main.nf.test.snap | 758 ++++++++++++++++++ .../bcftools/norm/tests/nextflow.bcf.config | 4 + .../norm/tests/nextflow.bcf_gz.config | 4 + .../bcftools/norm/tests/nextflow.config | 4 + .../bcftools/norm/tests/nextflow.vcf.config | 4 + .../norm/tests/nextflow.vcf_gz.config | 4 + modules/nf-core/bcftools/norm/tests/tags.yml | 2 + .../bcftools/norm/tests/vcf_gz_index.config | 4 + .../norm/tests/vcf_gz_index_csi.config | 4 + .../norm/tests/vcf_gz_index_tbi.config | 4 + .../bcftools/pluginscatter/environment.yml | 2 +- .../nf-core/bcftools/pluginscatter/main.nf | 24 +- .../nf-core/bcftools/pluginscatter/meta.yml | 8 + .../bcftools/pluginscatter/tests/main.nf.test | 415 ++++++++++ .../pluginscatter/tests/main.nf.test.snap | 623 ++++++++++++++ .../pluginscatter/tests/nextflow.config | 3 + .../bcftools/pluginscatter/tests/tags.yml | 2 + .../pluginscatter/tests/vcf_gz_index.config | 4 + .../tests/vcf_gz_index_csi.config | 4 + .../tests/vcf_gz_index_tbi.config | 4 + .../nf-core/bcftools/query/environment.yml | 2 +- modules/nf-core/bcftools/query/main.nf | 4 +- .../nf-core/bcftools/query/tests/main.nf.test | 16 +- .../bcftools/query/tests/main.nf.test.snap | 24 +- .../bcftools/reheader/bcftools-reheader.diff | 19 - .../nf-core/bcftools/reheader/environment.yml | 2 +- modules/nf-core/bcftools/reheader/main.nf | 15 +- modules/nf-core/bcftools/reheader/meta.yml | 4 + .../bcftools/reheader/tests/main.nf.test | 233 +++++- .../bcftools/reheader/tests/main.nf.test.snap | 345 +++++++- .../reheader/tests/vcf_gz_index.config | 4 + .../reheader/tests/vcf_gz_index_csi.config | 4 + .../reheader/tests/vcf_gz_index_tbi.config | 5 + modules/nf-core/bcftools/sort/environment.yml | 2 +- modules/nf-core/bcftools/sort/main.nf | 19 +- modules/nf-core/bcftools/sort/meta.yml | 8 + .../nf-core/bcftools/sort/tests/main.nf.test | 222 +++++ .../bcftools/sort/tests/main.nf.test.snap | 350 ++++++++ modules/nf-core/bcftools/sort/tests/tags.yml | 2 + .../bcftools/sort/tests/vcf_gz_index.config | 4 + .../sort/tests/vcf_gz_index_csi.config | 4 + .../sort/tests/vcf_gz_index_tbi.config | 4 + .../nf-core/bcftools/stats/environment.yml | 3 +- modules/nf-core/bcftools/stats/main.nf | 4 +- .../nf-core/bcftools/stats/tests/main.nf.test | 182 +++++ .../bcftools/stats/tests/main.nf.test.snap | 180 +++++ modules/nf-core/bcftools/stats/tests/tags.yml | 2 + .../download/ensemblvep-download.diff | 25 - .../ensemblvep/download/environment.yml | 2 +- modules/nf-core/ensemblvep/download/main.nf | 14 +- .../ensemblvep/download/tests/main.nf.test | 60 ++ .../download/tests/main.nf.test.snap | 322 ++++++++ .../ensemblvep/download/tests/nextflow.config | 12 + .../ensemblvep/download/tests/tags.yml | 2 + .../ensemblvep/vep/ensemblvep-vep.diff | 38 - .../nf-core/ensemblvep/vep/environment.yml | 4 +- modules/nf-core/ensemblvep/vep/main.nf | 18 +- modules/nf-core/ensemblvep/vep/meta.yml | 6 +- .../nf-core/ensemblvep/vep/tests/main.nf.test | 114 +++ .../ensemblvep/vep/tests/main.nf.test.snap | 26 + .../ensemblvep/vep/tests/nextflow.config | 12 + .../ensemblvep/vep/tests/tab.gz.config | 5 + modules/nf-core/ensemblvep/vep/tests/tags.yml | 2 + .../nf-core/ensemblvep/vep/tests/vcf.config | 5 + .../genotypegvcfs/gatk4-genotypegvcfs.diff | 13 - modules/nf-core/gatk4/genotypegvcfs/main.nf | 18 +- modules/nf-core/gatk4/genotypegvcfs/meta.yml | 29 +- .../gatk4/genotypegvcfs/tests/main.nf.test | 285 +++++++ .../genotypegvcfs/tests/main.nf.test.snap | 191 +++++ modules/nf-core/gatk4/haplotypecaller/main.nf | 4 +- .../gatk4/haplotypecaller/tests/main.nf.test | 86 +- .../haplotypecaller/tests/main.nf.test.snap | 88 +- modules/nf-core/gawk/environment.yml | 2 +- modules/nf-core/gawk/main.nf | 9 +- modules/nf-core/gawk/tests/main.nf.test | 56 ++ modules/nf-core/gawk/tests/main.nf.test.snap | 68 ++ modules/nf-core/gawk/tests/nextflow.config | 6 + .../tests/nextflow_with_program_file.config | 5 + modules/nf-core/gawk/tests/tags.yml | 2 + modules/nf-core/happy/happy/environment.yml | 7 - modules/nf-core/happy/happy/main.nf | 84 -- modules/nf-core/happy/happy/meta.yml | 114 --- modules/nf-core/mosdepth/environment.yml | 2 +- modules/nf-core/mosdepth/main.nf | 12 +- modules/nf-core/mosdepth/tests/main.nf.test | 66 +- .../nf-core/mosdepth/tests/main.nf.test.snap | 423 +++++++--- modules/nf-core/rtgtools/pedfilter/main.nf | 12 +- modules/nf-core/rtgtools/pedfilter/meta.yml | 2 +- .../pedfilter/rtgtools-pedfilter.diff | 40 +- .../rtgtools/pedfilter/tests/main.nf.test | 85 ++ .../pedfilter/tests/main.nf.test.snap | 91 +++ .../rtgtools/pedfilter/tests/nextflow.config | 5 + modules/nf-core/rtgtools/rocplot/meta.yml | 2 +- .../rtgtools/rocplot/tests/main.nf.test | 16 +- .../rtgtools/rocplot/tests/main.nf.test.snap | 6 +- .../nf-core/samtools/convert/environment.yml | 4 +- modules/nf-core/samtools/convert/main.nf | 26 +- modules/nf-core/samtools/convert/meta.yml | 19 +- .../samtools/convert/tests/main.nf.test | 44 +- .../samtools/convert/tests/main.nf.test.snap | 119 ++- .../nf-core/samtools/faidx/environment.yml | 6 +- modules/nf-core/samtools/faidx/main.nf | 4 +- modules/nf-core/samtools/faidx/meta.yml | 4 + .../nf-core/samtools/faidx/tests/main.nf.test | 122 +++ .../samtools/faidx/tests/main.nf.test.snap | 249 ++++++ .../samtools/faidx/tests/nextflow.config | 7 + .../samtools/faidx/tests/nextflow2.config | 6 + modules/nf-core/samtools/faidx/tests/tags.yml | 2 + .../nf-core/samtools/index/environment.yml | 4 +- modules/nf-core/samtools/index/main.nf | 11 +- .../nf-core/samtools/index/tests/main.nf.test | 87 +- .../samtools/index/tests/main.nf.test.snap | 264 +++++- .../nf-core/samtools/merge/environment.yml | 4 +- modules/nf-core/samtools/merge/main.nf | 4 +- .../samtools/merge/samtools-merge.diff | 13 - .../samtools/merge/tests/main.nf.test.snap | 24 +- modules/nf-core/snpeff/snpeff/main.nf | 10 +- .../nf-core/snpeff/snpeff/tests/main.nf.test | 51 ++ .../snpeff/snpeff/tests/main.nf.test.snap | 31 + .../snpeff/snpeff/tests/nextflow.config | 4 + modules/nf-core/snpeff/snpeff/tests/tags.yml | 2 + .../nf-core/somalier/extract/environment.yml | 2 +- modules/nf-core/somalier/extract/main.nf | 10 +- modules/nf-core/somalier/extract/meta.yml | 17 +- .../somalier/extract/tests/main.nf.test | 84 ++ .../somalier/extract/tests/main.nf.test.snap | 72 ++ .../nf-core/somalier/extract/tests/tags.yml | 2 + .../nf-core/somalier/relate/environment.yml | 2 +- modules/nf-core/somalier/relate/main.nf | 4 +- modules/nf-core/somalier/relate/meta.yml | 4 +- .../somalier/relate/somalier-relate.diff | 6 + .../somalier/relate/tests/main.nf.test | 124 +++ .../somalier/relate/tests/main.nf.test.snap | 286 +++++++ .../nf-core/somalier/relate/tests/tags.yml | 2 + modules/nf-core/tabix/bgzip/environment.yml | 1 + modules/nf-core/tabix/bgzip/main.nf | 7 +- .../tabix/bgzip/tests/bgzip_compress.config | 5 + .../nf-core/tabix/bgzip/tests/main.nf.test | 111 +++ 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modules/nf-core/untar/main.nf | 29 +- modules/nf-core/untar/tests/main.nf.test | 44 +- modules/nf-core/untar/tests/main.nf.test.snap | 152 +++- modules/nf-core/vardictjava/environment.yml | 1 + modules/nf-core/vardictjava/main.nf | 15 +- modules/nf-core/vardictjava/meta.yml | 2 +- .../nf-core/vardictjava/tests/main.nf.test | 24 +- .../vardictjava/tests/main.nf.test.snap | 20 +- modules/nf-core/vardictjava/vardictjava.diff | 13 - modules/nf-core/vcf2db/Dockerfile | 11 - modules/nf-core/vcf2db/main.nf | 10 +- modules/nf-core/vcf2db/tests/main.nf.test | 14 +- .../nf-core/vcf2db/tests/main.nf.test.snap | 40 +- modules/nf-core/vcf2db/vcf2db.diff | 143 ---- modules/nf-core/vcf2db/vcf2db_env.yaml | 96 --- nextflow.config | 3 +- nextflow_schema.json | 10 +- .../local/cram_call_vardictjava/main.nf | 8 +- .../local/gvcf_joint_genotype_gatk4/main.nf | 6 +- .../local/vcf_extract_relate_somalier/main.nf | 6 +- .../local/vcf_validate_small_variants/main.nf | 171 ++-- tests/pipeline/callers/main.nf.test.snap | 38 +- tests/pipeline/default/main.nf.test.snap | 12 +- tests/pipeline/gvcfs/main.nf.test.snap | 9 +- tests/pipeline/variations/main.nf.test.snap | 71 +- tests/pipeline/variations2/main.nf.test.snap | 60 +- .../cram_call_genotype_gatk4/main.nf.test | 40 +- .../main.nf.test.snap | 40 +- .../local/cram_call_vardictjava/main.nf.test | 12 +- .../local/vcf_annotation/main.nf.test.snap | 24 +- .../vcf_extract_relate_somalier/main.nf.test | 12 +- .../vcf_validate_small_variants/main.nf.test | 13 - .../main.nf.test.snap | 33 +- workflows/germline.nf | 24 +- 235 files changed, 11083 insertions(+), 1749 deletions(-) create mode 120000 CITATIONS.md create mode 100644 modules/nf-core/bcftools/annotate/bcftools-annotate.diff create mode 100644 modules/nf-core/bcftools/annotate/tests/bcf.config create mode 100644 modules/nf-core/bcftools/annotate/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/annotate/tests/main.nf.test.snap create mode 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modules/nf-core/tabix/tabix/tests/main.nf.test create mode 100644 modules/nf-core/tabix/tabix/tests/main.nf.test.snap create mode 100644 modules/nf-core/tabix/tabix/tests/tabix_bed.config create mode 100644 modules/nf-core/tabix/tabix/tests/tabix_gff.config create mode 100644 modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config create mode 100644 modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config create mode 100644 modules/nf-core/tabix/tabix/tests/tags.yml delete mode 100644 modules/nf-core/vardictjava/vardictjava.diff delete mode 100644 modules/nf-core/vcf2db/Dockerfile delete mode 100644 modules/nf-core/vcf2db/vcf2db.diff delete mode 100644 modules/nf-core/vcf2db/vcf2db_env.yaml diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 49fb4340..9593436d 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,6 +1,6 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure +# It runs the `nf-core pipelines lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: push: @@ -41,17 +41,24 @@ jobs: python-version: "3.12" architecture: "x64" + - name: read .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.0.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yaml + - name: Install dependencies run: | python -m pip install --upgrade pip pip install git+https://github.com/nf-core/tools@dev + #pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - - name: Run nf-core lint + - name: Run nf-core pipelines lint env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Save PR number if: ${{ always() }} diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 40acc23f..42e519bf 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 + uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.nf-core.yml b/.nf-core.yml index f9c0a042..d6b21f91 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,24 +1,34 @@ lint: files_exist: - - CODE_OF_CONDUCT.md - - assets/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_dark.png - - .github/ISSUE_TEMPLATE/config.yml - - .github/workflows/awstest.yml - - .github/workflows/awsfulltest.yml + - "CODE_OF_CONDUCT.md" + - "assets/nf-core-germline_logo_light.png" + - "docs/images/nf-core-germline_logo_light.png" + - "docs/images/nf-core-germline_logo_dark.png" + - ".github/ISSUE_TEMPLATE/config.yml" + - ".github/workflows/awstest.yml" + - ".github/workflows/awsfulltest.yml" + - "docs/README.md" files_unchanged: - - CODE_OF_CONDUCT.md - - assets/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_light.png - - docs/images/nf-core-germline_logo_dark.png - - .github/ISSUE_TEMPLATE/bug_report.yml - multiqc_config: - - report_comment + - ".github/CONTRIBUTING.md" + - ".github/PULL_REQUEST_TEMPLATE.md" + - ".github/workflows/linting_comment.yml" + - ".github/workflows/linting.yml" + - "CODE_OF_CONDUCT.md" + - ".github/ISSUE_TEMPLATE/bug_report.yml" + - ".prettierignore" nextflow_config: - - manifest.name - - manifest.homePage -nf_core_version: 2.14.1 + - "custom_config" # TODO Remove this once the new methods are supported + - "manifest.name" + - "manifest.homePage" + - "params.genomes" + - "validation.help.beforeText" + - "validation.help.afterText" + - "validation.summary.beforeText" + - "validation.summary.afterText" + multiqc_config: + - "report_comment" + actions_ci: false # TODO readd this once the linting doesn't act up +nf_core_version: 3.0.0dev repository_type: pipeline template: author: nvnieuwk diff --git a/CHANGELOG.md b/CHANGELOG.md index 0e59e9f4..50d6471f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## Changes 1. Bumped the minimal support nextflow version to `24.04.0` +2. Bumped all modules to the newest versions +3. The pipeline now also outputs `csi` indices ## Refactors diff --git a/CITATIONS.md b/CITATIONS.md new file mode 120000 index 00000000..35cfd9f8 --- /dev/null +++ b/CITATIONS.md @@ -0,0 +1 @@ +docs/CITATIONS.md \ No newline at end of file diff --git a/README.md b/README.md index ed28ef68..bd133931 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![GitHub Actions Linting Status](https://github.com/nf-cmgg/germline/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-cmgg/germline/actions/workflows/linting.yml) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) diff --git a/conf/modules.config b/conf/modules.config index f8f93e8f..917f26c0 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -333,7 +333,7 @@ process { } withName: "^.*CRAM_CALL_VARDICTJAVA:VCF_FILTER_BCFTOOLS:FILTER_2\$" { - ext.args = "--soft-filter 'LowFreqBias' --mode '+' -e 'FORMAT/AF[0] < 0.02 && FORMAT/VD[0] < 30 && INFO/SBF < 0.1 && INFO/NM >= 2.0' --output-type z" + ext.args = "--soft-filter 'LowFreqBias' --mode '+' -e 'FORMAT/AF[0:*] < 0.02 && FORMAT/VD[0] < 30 && INFO/SBF < 0.1 && INFO/NM >= 2.0' --output-type z" ext.prefix = enableOutput("filter") ? final_prefix : {"${meta.id}.filtered"} publishDir = [ overwrite: true, diff --git a/conf/test_full.config b/conf/test_full.config index 9943a39d..37b1a6c0 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -15,9 +15,7 @@ params { config_profile_description = 'Full test dataset to check pipeline function' // Input data for full size test - // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) - // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' + // input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' // Genome references genome = 'R64-1-1' diff --git a/main.nf b/main.nf index b64b8d83..988afc56 100644 --- a/main.nf +++ b/main.nf @@ -194,7 +194,7 @@ workflow { def multiqc_logo = params.multiqc_logo ?: "$projectDir/assets/CMGG_logo.png" - + print(params.genomes) // // SUBWORKFLOW: Run initialisation tasks // diff --git a/modules.json b/modules.json index 1e2993d5..b9a65237 100644 --- a/modules.json +++ b/modules.json @@ -7,49 +7,48 @@ "nf-core": { "bcftools/annotate": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": ["modules"] + "git_sha": "88ae68490e8f2478a1e1bbeedac970fd7cc73022", + "installed_by": ["modules"], + "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff" }, "bcftools/concat": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff"], - "patch": "modules/nf-core/bcftools/concat/bcftools-concat.diff" + "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/filter": { "branch": "master", - "git_sha": "a3893076a76e91b3ff152faddf872f00778fb224", + "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988", "installed_by": ["modules"] }, "bcftools/norm": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", + "git_sha": "f6cc00f107826cfaf1c933297b10ed1757b41479", "installed_by": ["modules"] }, "bcftools/pluginscatter": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", + "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/query": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", + "git_sha": "34ac993e081b32d2170ab790d0386b74122f9d36", "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": ["modules"], - "patch": "modules/nf-core/bcftools/reheader/bcftools-reheader.diff" + "git_sha": "c32611ac6813055b9321d2827678e2f8aebcb394", + "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", + "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/stats": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", + "git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f", "installed_by": ["modules"] }, "bedtools/intersect": { @@ -59,71 +58,62 @@ }, "bedtools/merge": { "branch": "master", - "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", + "git_sha": "a3d614e4a7b8691a259bcfe33ad80903217d6215", "installed_by": ["modules"] }, "bedtools/split": { "branch": "master", - "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", + "git_sha": "6dc8a32e32158bb4d3f9af92c802233b5d4f8e4d", "installed_by": ["modules"] }, "ensemblvep/download": { "branch": "master", - "git_sha": "214d575774c172062924ad3564b4f66655600730", - "installed_by": ["modules"], - "patch": "modules/nf-core/ensemblvep/download/ensemblvep-download.diff" + "git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0", + "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", - "git_sha": "1b5ffd7aa6e3c21b702957c808cbd1c351dd1809", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"], - "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" + "git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0", + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "gatk4/calibratedragstrmodel": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", + "git_sha": "3f42e07a1133064c569b0dbe182979527bca9e59", "installed_by": ["modules"] }, "gatk4/composestrtablefile": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", + "git_sha": "926e2f394d01c71d3abbdbca9c588630bfe51abf", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", + "git_sha": "e6fe277739f5894711405af3e717b2470bd956b5", "installed_by": ["modules"] }, "gatk4/genomicsdbimport": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", "installed_by": ["modules"] }, "gatk4/genotypegvcfs": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", - "installed_by": ["modules"], - "patch": "modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff" + "git_sha": "8b74c800af3d91e0d7bfbecb902308dc4369071c", + "installed_by": ["modules"] }, "gatk4/haplotypecaller": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", - "installed_by": ["modules"], - "patch": "modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff" + "git_sha": "c332ea831f95f750be962c4b5de655f7a1e6e245", + "installed_by": ["modules"] }, "gawk": { "branch": "master", - "git_sha": "dc3527855e7358c6d8400828754c0caa5f11698f", - "installed_by": ["modules"] - }, - "happy/happy": { - "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", "installed_by": ["modules"] }, "mosdepth": { "branch": "master", - "git_sha": "69e3eb17fb31b772b18f134d6e8f8b93ee980e65", + "git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb", "installed_by": ["modules"] }, "multiqc": { @@ -138,13 +128,13 @@ }, "rtgtools/pedfilter": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "c1c2a770cfb0bfbf093a2434a27f091ebbc65987", "installed_by": ["modules"], "patch": "modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff" }, "rtgtools/rocplot": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "64770369d851c45c364e410e052ef9a6c3a7d2bb", "installed_by": ["modules"] }, "rtgtools/vcfeval": { @@ -154,76 +144,73 @@ }, "samtools/convert": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": ["modules"] }, "samtools/index": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["modules"], - "patch": "modules/nf-core/samtools/merge/samtools-merge.diff" + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", + "installed_by": ["modules"] }, "snpeff/snpeff": { "branch": "master", - "git_sha": "214d575774c172062924ad3564b4f66655600730", + "git_sha": "3ad7292d9b8da881386e9d5b58364d7da489b38b", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "somalier/extract": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "458c882987320e27fc90723ec96c127a243a5497", "installed_by": ["modules"] }, "somalier/relate": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "458c882987320e27fc90723ec96c127a243a5497", "installed_by": ["modules"], "patch": "modules/nf-core/somalier/relate/somalier-relate.diff" }, "tabix/bgzip": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "b20be35facfc5acdc1259f132ed79339d79e989f", "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", "installed_by": ["modules"] }, "tabix/tabix": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff"] }, "untar": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", "installed_by": ["modules"] }, "vardictjava": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"], - "patch": "modules/nf-core/vardictjava/vardictjava.diff" + "git_sha": "e61e5a13ef49c5595986bd31efb85c3f0709a282", + "installed_by": ["modules"] }, "vcf2db": { "branch": "master", - "git_sha": "527a80a28d9a54e5fd3626168ab72b063c11fbb2", - "installed_by": ["modules"], - "patch": "modules/nf-core/vcf2db/vcf2db.diff" + "git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006", + "installed_by": ["modules"] }, "vcfanno": { "branch": "master", - "git_sha": "b558cd24f8751dcda51f957391f5f9cb83e28586", + "git_sha": "9a8bba5910982ae637dedb8664e3121db77e173f", "installed_by": ["modules"] } } diff --git a/modules/nf-core/bcftools/annotate/bcftools-annotate.diff b/modules/nf-core/bcftools/annotate/bcftools-annotate.diff new file mode 100644 index 00000000..518cee56 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/bcftools-annotate.diff @@ -0,0 +1,26 @@ +Changes in module 'nf-core/bcftools/annotate' +Changes in 'bcftools/annotate/main.nf': +--- modules/nf-core/bcftools/annotate/main.nf ++++ modules/nf-core/bcftools/annotate/main.nf +@@ -8,8 +8,7 @@ + 'biocontainers/bcftools:1.20--h8b25389_0' }" + + input: +- tuple val(meta), path(input), path(index), path(annotations), path(annotations_index) +- path(header_lines) ++ tuple val(meta), path(input), path(index), path(annotations), path(annotations_index), path(header_lines) + + output: + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + +'modules/nf-core/bcftools/annotate/environment.yml' is unchanged +'modules/nf-core/bcftools/annotate/meta.yml' is unchanged +'modules/nf-core/bcftools/annotate/tests/tags.yml' is unchanged +'modules/nf-core/bcftools/annotate/tests/vcf.config' is unchanged +'modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config' is unchanged +'modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config' is unchanged +'modules/nf-core/bcftools/annotate/tests/main.nf.test' is unchanged +'modules/nf-core/bcftools/annotate/tests/bcf.config' is unchanged +'modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config' is unchanged +'modules/nf-core/bcftools/annotate/tests/main.nf.test.snap' is unchanged +************************************************************ diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml index e0abc8d2..3d4e3379 100644 --- a/modules/nf-core/bcftools/annotate/environment.yml +++ b/modules/nf-core/bcftools/annotate/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index 27ebfd4a..2cfe29a1 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -4,14 +4,16 @@ process BCFTOOLS_ANNOTATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(input), path(index), path(annotations), path(annotations_index), path(header_lines) output: tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true path "versions.yml" , emit: versions when: @@ -27,8 +29,12 @@ process BCFTOOLS_ANNOTATE { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + def index_command = !index ? "bcftools index $input" : '' + if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" """ + $index_command + bcftools \\ annotate \\ $args \\ @@ -52,8 +58,16 @@ process BCFTOOLS_ANNOTATE { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + """ - touch ${prefix}.${extension} + ${create_cmd} ${prefix}.${extension} + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/annotate/meta.yml b/modules/nf-core/bcftools/annotate/meta.yml index f3aa463b..248eee0c 100644 --- a/modules/nf-core/bcftools/annotate/meta.yml +++ b/modules/nf-core/bcftools/annotate/meta.yml @@ -40,14 +40,22 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: type: file description: Compressed annotated VCF file pattern: "*{vcf,vcf.gz,bcf,bcf.gz}" + - csi: + type: file + description: Default VCF file index + pattern: "*.csi" + - tbi: + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@projectoriented" - "@ramprasadn" diff --git a/modules/nf-core/bcftools/annotate/tests/bcf.config b/modules/nf-core/bcftools/annotate/tests/bcf.config new file mode 100644 index 00000000..79d26779 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/bcf.config @@ -0,0 +1,4 @@ +process { + ext.args = "-x ID,INFO/DP,FORMAT/DP --output-type u" + ext.prefix = { "${meta.id}_ann" } +} diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test b/modules/nf-core/bcftools/annotate/tests/main.nf.test new file mode 100644 index 00000000..3a5c4933 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test @@ -0,0 +1,327 @@ +nextflow_process { + + name "Test Process BCFTOOLS_ANNOTATE" + script "../main.nf" + process "BCFTOOLS_ANNOTATE" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/annotate" + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output") { + + config "./vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output") { + + config "./vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.versions + ).match() } + ) + } + + } + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + test("sarscov2 - [vcf, [], annotation, annotation_tbi], header - bcf_output") { + + config "./bcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = Channel.of( + '##INFO=', + '##INFO=' + ).collectFile(name:"headers.vcf", newLine:true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.versions + ).match("bcf") } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub") { + + config "./vcf.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match()}, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap new file mode 100644 index 00000000..bac2224a --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap @@ -0,0 +1,388 @@ +{ + "bcf": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_ann.bcf" + ] + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-12T16:39:33.331888" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:07:59.658031137" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:09:05.096883418" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:08:10.581301219" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:08:43.975017625" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi" + ] + ], + [ + + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:08:21.354059092" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_output": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:07:37.788393317" + }, + "sarscov2 - [vcf, [], annotation, annotation_tbi], [] - vcf_output": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:07:48.500746325" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:09:16.094918834" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [] - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-08-15T10:08:54.366358502" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/annotate/tests/tags.yml b/modules/nf-core/bcftools/annotate/tests/tags.yml new file mode 100644 index 00000000..f97a1afc --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/annotate: + - "modules/nf-core/bcftools/annotate/**" diff --git a/modules/nf-core/bcftools/annotate/tests/vcf.config b/modules/nf-core/bcftools/annotate/tests/vcf.config new file mode 100644 index 00000000..611868d5 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/vcf.config @@ -0,0 +1,4 @@ +process { + ext.args = "-x ID,INFO/DP,FORMAT/DP --output-type z" + ext.prefix = { "${meta.id}_vcf" } +} diff --git a/modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config new file mode 100644 index 00000000..2fd9a225 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.args = "--output-type z --write-index --no-version" + ext.prefix = { "${meta.id}_vcf" } +} diff --git a/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..512c1dfb --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.args = "--output-type z --write-index=csi --no-version" + ext.prefix = { "${meta.id}_vcf" } +} diff --git a/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..7feb5ebb --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.args = "--output-type z --write-index=tbi --no-version" + ext.prefix = { "${meta.id}_vcf" } +} diff --git a/modules/nf-core/bcftools/concat/bcftools-concat.diff b/modules/nf-core/bcftools/concat/bcftools-concat.diff deleted file mode 100644 index 980df77a..00000000 --- a/modules/nf-core/bcftools/concat/bcftools-concat.diff +++ /dev/null @@ -1,40 +0,0 @@ -Changes in module 'nf-core/bcftools/concat' ---- modules/nf-core/bcftools/concat/main.nf -+++ modules/nf-core/bcftools/concat/main.nf -@@ -8,7 +8,7 @@ - 'biocontainers/bcftools:1.18--h8b25389_0' }" - - input: -- tuple val(meta), path(vcfs), path(tbi) -+ tuple val(meta), path(vcfs), path(tbis) - - output: - tuple val(meta), path("*.gz"), emit: vcf -@@ -19,8 +19,11 @@ - - script: - def args = task.ext.args ?: '' -- prefix = task.ext.prefix ?: "${meta.id}" -+ def prefix = task.ext.prefix ?: "${meta.id}" -+ def create_tbis = vcfs.collect { it.extension == 'gz' && !tbis ? " tabix ${it}" : "" } -+ - """ -+ ${create_tbis.join("\n")} - bcftools concat \\ - --output ${prefix}.vcf.gz \\ - $args \\ -@@ -34,8 +37,11 @@ - """ - - stub: -- prefix = task.ext.prefix ?: "${meta.id}" -+ def prefix = task.ext.prefix ?: "${meta.id}" -+ def create_tbis = vcfs.collect { it.extension == 'gz' && !tbis ? " touch ${it}.tbi" : "" } -+ - """ -+ ${create_tbis.join("\n")} - touch ${prefix}.vcf.gz - - cat <<-END_VERSIONS > versions.yml - -************************************************************ diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml index ff0200df..6544e949 100644 --- a/modules/nf-core/bcftools/concat/environment.yml +++ b/modules/nf-core/bcftools/concat/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index eaefbe73..e2337eff 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -4,26 +4,25 @@ process BCFTOOLS_CONCAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: - tuple val(meta), path(vcfs), path(tbis) + tuple val(meta), path(vcfs), path(tbi) output: - tuple val(meta), path("*.gz"), emit: vcf - path "versions.yml" , emit: versions + tuple val(meta), path("*.gz") , emit: vcf + tuple val(meta), path("*.tbi"), emit: tbi, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def create_tbis = vcfs.collect { it.extension == 'gz' && !tbis ? " tabix ${it}" : "" } - + def prefix = task.ext.prefix ?: "${meta.id}" """ - ${create_tbis.join("\n")} bcftools concat \\ --output ${prefix}.vcf.gz \\ $args \\ @@ -37,12 +36,16 @@ process BCFTOOLS_CONCAT { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" - def create_tbis = vcfs.collect { it.extension == 'gz' && !tbis ? " touch ${it}.tbi" : "" } - + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_index = index.matches("csi|tbi") ? "touch ${prefix}.vcf.gz.${index}" : "" """ - ${create_tbis.join("\n")} - touch ${prefix}.vcf.gz + echo "" | gzip > ${prefix}.vcf.gz + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml index 91cb54d5..eeeb2071 100644 --- a/modules/nf-core/bcftools/concat/meta.yml +++ b/modules/nf-core/bcftools/concat/meta.yml @@ -39,6 +39,14 @@ output: type: file description: VCF concatenated output file pattern: "*.{vcf.gz}" + - csi: + type: file + description: Default VCF file index + pattern: "*.csi" + - tbi: + type: file + description: Alternative VCF file index + pattern: "*.tbi" - versions: type: file description: File containing software versions diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test b/modules/nf-core/bcftools/concat/tests/main.nf.test index bf1a5f3f..cea386e3 100644 --- a/modules/nf-core/bcftools/concat/tests/main.nf.test +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test @@ -9,22 +9,54 @@ nextflow_process { tag "bcftools" tag "bcftools/concat" - config "./nextflow.config" test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]") { + config "./nextflow.config" + when { process { """ - input[0] = [ + input[0] = [ [ id:'test3' ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) ], [ - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) ] ] """ @@ -36,25 +68,33 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.versions - ).match() } + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } ) } } - test("sarscov2 - [[vcf1, vcf2], []]") { + test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" when { process { """ - input[0] = [ + input[0] = [ [ id:'test3' ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) ], - [] + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] ] """ } @@ -65,28 +105,32 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.versions - ).match() } + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } ) } } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub") { + test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" - options "-stub" when { process { """ - input[0] = [ + input[0] = [ [ id:'test3' ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) ], [ - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) ] ] """ @@ -97,12 +141,176 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - file(process.out.vcf[0][1]).name, + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, process.out.versions - ).match() } + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + + test("sarscov2 - [[vcf1, vcf2], []]") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } ) } } -} + test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap index 7344e6e3..1182854f 100644 --- a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap @@ -1,43 +1,395 @@ { + "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T08:09:13.734103412" + }, "sarscov2 - [[vcf1, vcf2], []]": { "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + "versions": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T15:19:09.213249578" + }, + "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], [ [ { "id": "test3" }, - "test3.vcf.gz:md5,4bcd0afd89f56c5d433f6b6abc44d0a6" + "test3_vcf.vcf.gz.csi" ] ], [ - "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + + ], + [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" ] ], - "timestamp": "2023-11-29T13:52:27.03724666" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T08:08:23.981388325" + }, + "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T14:01:24.419027693" }, "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]": { "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + "versions": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T15:19:03.597061078" + }, + "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], [ [ { "id": "test3" }, - "test3.vcf.gz:md5,4bcd0afd89f56c5d433f6b6abc44d0a6" + "test3_vcf.vcf.gz.csi" ] ], [ - "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + + ], + [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" ] ], - "timestamp": "2023-11-29T13:52:21.468988293" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T14:00:10.868487669" }, "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub": { "content": [ - "test3.vcf.gz", + { + "0": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T15:19:14.836256897" + }, + "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi": { + "content": [ [ - "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + [ + + ], + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" ] ], - "timestamp": "2023-11-29T13:41:04.716017811" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T14:00:31.061411617" + }, + "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T14:01:35.209746508" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/concat/tests/vcf_gz_index.config b/modules/nf-core/bcftools/concat/tests/vcf_gz_index.config new file mode 100644 index 00000000..7dd696ee --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index --no-version" +} diff --git a/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..aebffb6f --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi --no-version" +} diff --git a/modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..b192ae7d --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi --no-version" +} diff --git a/modules/nf-core/bcftools/filter/environment.yml b/modules/nf-core/bcftools/filter/environment.yml index b2698757..854de139 100644 --- a/modules/nf-core/bcftools/filter/environment.yml +++ b/modules/nf-core/bcftools/filter/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf index cc9a2361..8f92c51a 100644 --- a/modules/nf-core/bcftools/filter/main.nf +++ b/modules/nf-core/bcftools/filter/main.nf @@ -4,14 +4,16 @@ process BCFTOOLS_FILTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcf) output: tuple val(meta), path("*.${extension}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true path "versions.yml" , emit: versions when: @@ -45,19 +47,23 @@ process BCFTOOLS_FILTER { stub: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" - def create_file = extension.endsWith(".gz") ? "echo '' | gzip > ${prefix}.${extension}" : "touch ${prefix}.${extension}" - """ - ${create_file} + ${create_cmd} ${prefix}.${extension} + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/filter/meta.yml b/modules/nf-core/bcftools/filter/meta.yml index deb93b13..d67c0257 100644 --- a/modules/nf-core/bcftools/filter/meta.yml +++ b/modules/nf-core/bcftools/filter/meta.yml @@ -32,6 +32,14 @@ output: type: file description: VCF filtered output file pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - csi: + type: file + description: Default VCF file index + pattern: "*.csi" + - tbi: + type: file + description: Alternative VCF file index + pattern: "*.tbi" - versions: type: file description: File containing software versions diff --git a/modules/nf-core/bcftools/filter/tests/main.nf.test b/modules/nf-core/bcftools/filter/tests/main.nf.test index eaf100e8..646f37ad 100644 --- a/modules/nf-core/bcftools/filter/tests/main.nf.test +++ b/modules/nf-core/bcftools/filter/tests/main.nf.test @@ -9,10 +9,10 @@ nextflow_process { tag "bcftools" tag "bcftools/filter" - config "./nextflow.config" - test("sarscov2 - vcf") { + config "./nextflow.config" + when { process { """ @@ -33,8 +33,100 @@ nextflow_process { } + test("sarscov2 - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + test("sarscov2 - vcf - bcf output") { + config "./nextflow.config" + when { process { """ @@ -57,6 +149,7 @@ nextflow_process { test("sarscov2 - vcf - stub") { + config "./nextflow.config" options "-stub" when { @@ -79,4 +172,82 @@ nextflow_process { } -} + test("sarscov2 - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/filter/tests/main.nf.test.snap b/modules/nf-core/bcftools/filter/tests/main.nf.test.snap index f8e17aa0..3d7605f2 100644 --- a/modules/nf-core/bcftools/filter/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/filter/tests/main.nf.test.snap @@ -1,4 +1,59 @@ { + "sarscov2 - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T13:59:08.235854993" + }, "vcf": { "content": [ { @@ -11,7 +66,19 @@ ] ], "1": [ - "versions.yml:md5,7dc77043f9afb848d942d47a7bc19f67" + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ], + "csi": [ + + ], + "tbi": [ + ], "vcf": [ [ @@ -22,15 +89,15 @@ ] ], "versions": [ - "versions.yml:md5,7dc77043f9afb848d942d47a7bc19f67" + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-27T16:57:32.940161987" + "timestamp": "2024-06-04T15:20:28.427974818" }, "bcf output": { "content": [ @@ -44,7 +111,19 @@ ] ], "1": [ - "versions.yml:md5,7dc77043f9afb848d942d47a7bc19f67" + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ], + "csi": [ + + ], + "tbi": [ + ], "vcf": [ [ @@ -55,15 +134,77 @@ ] ], "versions": [ - "versions.yml:md5,7dc77043f9afb848d942d47a7bc19f67" + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T15:20:34.049236749" + }, + "sarscov2 - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" }, - "timestamp": "2024-03-27T16:45:14.586866398" + "timestamp": "2024-06-05T08:09:49.837854646" + }, + "sarscov2 - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T13:57:19.513365022" }, "vcf - stub": { "content": [ @@ -77,7 +218,19 @@ ] ], "1": [ - "versions.yml:md5,7dc77043f9afb848d942d47a7bc19f67" + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ], + "csi": [ + + ], + "tbi": [ + ], "vcf": [ [ @@ -88,14 +241,155 @@ ] ], "versions": [ - "versions.yml:md5,7dc77043f9afb848d942d47a7bc19f67" + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T15:29:55.846566153" + }, + "sarscov2 - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ], + "csi": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T15:59:37.636874258" + }, + "sarscov2 - vcf_gz_index_csi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ], + "csi": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T13:58:46.36278584" + }, + "sarscov2 - vcf_gz_index_tbi": { + "content": [ + [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + + ], + [ + [ + { + "id": "vcf_test" + }, + "vcf_test_vcf.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" }, - "timestamp": "2024-03-27T17:05:52.80837892" + "timestamp": "2024-06-05T13:57:34.748836577" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/filter/tests/vcf_gz_index.config b/modules/nf-core/bcftools/filter/tests/vcf_gz_index.config new file mode 100644 index 00000000..7dd696ee --- /dev/null +++ b/modules/nf-core/bcftools/filter/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index --no-version" +} diff --git a/modules/nf-core/bcftools/filter/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/filter/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..aebffb6f --- /dev/null +++ b/modules/nf-core/bcftools/filter/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi --no-version" +} diff --git a/modules/nf-core/bcftools/filter/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/filter/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..b192ae7d --- /dev/null +++ b/modules/nf-core/bcftools/filter/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi --no-version" +} diff --git a/modules/nf-core/bcftools/norm/environment.yml b/modules/nf-core/bcftools/norm/environment.yml index fe80e4e7..0c7dfa8f 100644 --- a/modules/nf-core/bcftools/norm/environment.yml +++ b/modules/nf-core/bcftools/norm/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/norm/main.nf b/modules/nf-core/bcftools/norm/main.nf index 47d3dab1..bd7a2501 100644 --- a/modules/nf-core/bcftools/norm/main.nf +++ b/modules/nf-core/bcftools/norm/main.nf @@ -4,16 +4,18 @@ process BCFTOOLS_NORM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcf), path(tbi) tuple val(meta2), path(fasta) output: - tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}") , emit: vcf - path "versions.yml" , emit: versions + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -30,7 +32,7 @@ process BCFTOOLS_NORM { """ bcftools norm \\ --fasta-ref ${fasta} \\ - --output ${prefix}.${extension}\\ + --output ${prefix}.${extension} \\ $args \\ --threads $task.cpus \\ ${vcf} @@ -49,8 +51,16 @@ process BCFTOOLS_NORM { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf.gz" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + """ - touch ${prefix}.${extension} + ${create_cmd} ${prefix}.${extension} + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/norm/meta.yml b/modules/nf-core/bcftools/norm/meta.yml index 1f3e1b62..a0cdeaf1 100644 --- a/modules/nf-core/bcftools/norm/meta.yml +++ b/modules/nf-core/bcftools/norm/meta.yml @@ -49,6 +49,14 @@ output: type: file description: One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - csi: + type: file + description: Default VCF file index + pattern: "*.csi" + - tbi: + type: file + description: Alternative VCF file index + pattern: "*.tbi" - versions: type: file description: File containing software versions diff --git a/modules/nf-core/bcftools/norm/tests/main.nf.test b/modules/nf-core/bcftools/norm/tests/main.nf.test new file mode 100644 index 00000000..dbc41502 --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/main.nf.test @@ -0,0 +1,563 @@ +nextflow_process { + + name "Test Process BCFTOOLS_NORM" + script "../main.nf" + process "BCFTOOLS_NORM" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/norm" + + test("sarscov2 - [ vcf, [] ], fasta") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } } + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } } + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } } + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta - vcf output") { + + config "./nextflow.vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta - vcf_gz output") { + + config "./nextflow.vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta - bcf output") { + + config "./nextflow.bcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta - bcf_gz output") { + + config "./nextflow.bcf_gz.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, [] ], fasta - stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta -stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta - vcf output -stub") { + + config "./nextflow.vcf.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta - vcf_gz output - stub") { + + config "./nextflow.vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta - bcf output - stub") { + + config "./nextflow.bcf.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, tbi ], fasta - bcf_gz output - stub") { + + config "./nextflow.bcf_gz.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/norm/tests/main.nf.test.snap b/modules/nf-core/bcftools/norm/tests/main.nf.test.snap new file mode 100644 index 00000000..3be52116 --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/main.nf.test.snap @@ -0,0 +1,758 @@ +{ + "sarscov2 - 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[ vcf, tbi ], fasta - bcf_gz output - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_norm.bcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,ff760495922469e56d0fc3372773000d" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_norm.bcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,ff760495922469e56d0fc3372773000d" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T14:39:10.503208929" + }, + "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,63e5adbaf3dd94550e9e3d7935dd28db" + ] + ], + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T07:52:58.381931979" + }, + "sarscov2 - [ vcf, tbi ], fasta - bcf output - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_norm.bcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,ff760495922469e56d0fc3372773000d" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_norm.bcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,ff760495922469e56d0fc3372773000d" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T14:38:59.121377258" + }, + "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,ff760495922469e56d0fc3372773000d" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,ff760495922469e56d0fc3372773000d" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T13:56:16.404380471" + }, + "sarscov2 - [ vcf, [] ], fasta - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,63e5adbaf3dd94550e9e3d7935dd28db" + ] + ], + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T13:53:09.808834237" + }, + "sarscov2 - [ vcf, tbi ], fasta - bcf output": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_norm.bcf.gz:md5,638c3c25bdd495c90ecbccb69ee77f07" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,ff760495922469e56d0fc3372773000d" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_norm.bcf.gz:md5,638c3c25bdd495c90ecbccb69ee77f07" + ] + ], + "versions": [ + "versions.yml:md5,ff760495922469e56d0fc3372773000d" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T14:37:42.141945244" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/norm/tests/nextflow.bcf.config b/modules/nf-core/bcftools/norm/tests/nextflow.bcf.config new file mode 100644 index 00000000..b79af868 --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/nextflow.bcf.config @@ -0,0 +1,4 @@ +process { + ext.args = '-m -any --output-type b --no-version' + ext.prefix = "test_norm" +} diff --git a/modules/nf-core/bcftools/norm/tests/nextflow.bcf_gz.config b/modules/nf-core/bcftools/norm/tests/nextflow.bcf_gz.config new file mode 100644 index 00000000..f36f397c --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/nextflow.bcf_gz.config @@ -0,0 +1,4 @@ +process { + ext.args = '-m -any --output-type u --no-version' + ext.prefix = "test_norm" +} diff --git a/modules/nf-core/bcftools/norm/tests/nextflow.config b/modules/nf-core/bcftools/norm/tests/nextflow.config new file mode 100644 index 00000000..510803b4 --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/nextflow.config @@ -0,0 +1,4 @@ +process { + ext.args = '-m -any --no-version' + ext.prefix = "test_norm" +} diff --git a/modules/nf-core/bcftools/norm/tests/nextflow.vcf.config b/modules/nf-core/bcftools/norm/tests/nextflow.vcf.config new file mode 100644 index 00000000..10bf93e3 --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/nextflow.vcf.config @@ -0,0 +1,4 @@ +process { + ext.args = '-m -any --output-type v --no-version' + ext.prefix = "test_norm" +} diff --git a/modules/nf-core/bcftools/norm/tests/nextflow.vcf_gz.config b/modules/nf-core/bcftools/norm/tests/nextflow.vcf_gz.config new file mode 100644 index 00000000..b31dd2de --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/nextflow.vcf_gz.config @@ -0,0 +1,4 @@ +process { + ext.args = '-m -any --output-type z ---no-version' + ext.prefix = "test_norm" +} diff --git a/modules/nf-core/bcftools/norm/tests/tags.yml b/modules/nf-core/bcftools/norm/tests/tags.yml new file mode 100644 index 00000000..f6f5e356 --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/norm: + - "modules/nf-core/bcftools/norm/**" diff --git a/modules/nf-core/bcftools/norm/tests/vcf_gz_index.config b/modules/nf-core/bcftools/norm/tests/vcf_gz_index.config new file mode 100644 index 00000000..7dd696ee --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index --no-version" +} diff --git a/modules/nf-core/bcftools/norm/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/norm/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..aebffb6f --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi --no-version" +} diff --git a/modules/nf-core/bcftools/norm/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/norm/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..b192ae7d --- /dev/null +++ b/modules/nf-core/bcftools/norm/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi --no-version" +} diff --git a/modules/nf-core/bcftools/pluginscatter/environment.yml b/modules/nf-core/bcftools/pluginscatter/environment.yml index 42e97daa..51bce4d3 100644 --- a/modules/nf-core/bcftools/pluginscatter/environment.yml +++ b/modules/nf-core/bcftools/pluginscatter/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/pluginscatter/main.nf b/modules/nf-core/bcftools/pluginscatter/main.nf index 9f52e947..b3b6691d 100644 --- a/modules/nf-core/bcftools/pluginscatter/main.nf +++ b/modules/nf-core/bcftools/pluginscatter/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_PLUGINSCATTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcf), path(tbi) @@ -17,6 +17,8 @@ process BCFTOOLS_PLUGINSCATTER { output: tuple val(meta), path("*{vcf,vcf.gz,bcf,bcf.gz}") , emit: scatter + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true path "versions.yml" , emit: versions when: @@ -57,11 +59,23 @@ process BCFTOOLS_PLUGINSCATTER { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index_1 = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}0.${extension}.${index}" : "" + def create_index_2 = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}1.${extension}.${index}" : "" + def create_index_3 = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}2.${extension}.${index}" : "" """ - touch ${prefix}1.${extension} - touch ${prefix}2.${extension} - touch ${prefix}3.${extension} + ${create_cmd} ${prefix}0.${extension} + ${create_cmd} ${prefix}1.${extension} + ${create_cmd} ${prefix}2.${extension} + + ${create_index_1} + ${create_index_2} + ${create_index_3} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/pluginscatter/meta.yml b/modules/nf-core/bcftools/pluginscatter/meta.yml index 1a716ead..71805c03 100644 --- a/modules/nf-core/bcftools/pluginscatter/meta.yml +++ b/modules/nf-core/bcftools/pluginscatter/meta.yml @@ -66,6 +66,14 @@ output: type: file description: The resulting files of the scattering pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - csi: + type: file + description: Default VCF file index + pattern: "*.csi" + - tbi: + type: file + description: Alternative VCF file index + pattern: "*.tbi" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test b/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test new file mode 100644 index 00000000..ce66336e --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test @@ -0,0 +1,415 @@ +nextflow_process { + + name "Test Process BCFTOOLS_PLUGINSCATTER" + script "../main.nf" + process "BCFTOOLS_PLUGINSCATTER" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/pluginscatter" + + test("homo_sapiens - sites per chunk") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match("vcf_gz_index") }, + { assert process.out.csi[0][1][0] =~ ".*/test_vcf0.vcf.gz.csi" } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match("vcf_gz_index_csi") }, + { assert process.out.csi[0][1][0] =~ ".*/test_vcf0.vcf.gz.csi" } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match("vcf_gz_index_tbi") }, + { assert process.out.tbi[0][1][0] =~ ".*/test_vcf0.vcf.gz.tbi" } + ) + } + + } + + test("homo_sapiens - scatter") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = "chr21" + input[3] = [] + input[4] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - scatter file") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + input[3] = Channel.of("chr21:6000000-41743940\tfile1", "chr21:41743941-46661900\tfile2") + .collectFile(name:"scatter.tsv", newLine:true) + input[4] = [] + input[5] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - sites per chunk - stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - scatter - stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = "chr21" + input[3] = [] + input[4] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - scatter file - stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + input[3] = Channel.of("chr21:6000000-41743940\tfile1", "chr21:41743941-46661900\tfile2") + .collectFile(name:"scatter.tsv", newLine:true) + input[4] = [] + input[5] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1][0] =~ ".*/test_vcf0.vcf.gz.csi" } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1][0] =~ ".*/test_vcf0.vcf.gz.csi" } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1][0] =~ ".*/test_vcf0.vcf.gz.tbi" } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test.snap new file mode 100644 index 00000000..3168f91b --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test.snap @@ -0,0 +1,623 @@ +{ + "homo_sapiens - 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scatter": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "testchr21.vcf:md5,68e3660b6d619163692edad8ba7dd179" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ], + "csi": [ + + ], + "scatter": [ + [ + { + "id": "test" + }, + "testchr21.vcf:md5,68e3660b6d619163692edad8ba7dd179" + ] + ], + "tbi": [ + + ], + "versions": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T14:40:12.621284696" + }, + "homo_sapiens - sites per chunk - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test0.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test1.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test2.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ], + "csi": [ + + ], + "scatter": [ + [ + { + "id": "test" + }, + [ + "test0.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test1.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test2.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "tbi": [ + + ], + "versions": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T15:08:56.987822348" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/pluginscatter/tests/nextflow.config b/modules/nf-core/bcftools/pluginscatter/tests/nextflow.config new file mode 100644 index 00000000..aa8d093b --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/nextflow.config @@ -0,0 +1,3 @@ +process { + ext.args = '--no-version' +} diff --git a/modules/nf-core/bcftools/pluginscatter/tests/tags.yml b/modules/nf-core/bcftools/pluginscatter/tests/tags.yml new file mode 100644 index 00000000..60cebd43 --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/pluginscatter: + - "modules/nf-core/bcftools/pluginscatter/**" diff --git a/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index.config b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index.config new file mode 100644 index 00000000..7dd696ee --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index --no-version" +} diff --git a/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..aebffb6f --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi --no-version" +} diff --git a/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..b192ae7d --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi --no-version" +} diff --git a/modules/nf-core/bcftools/query/environment.yml b/modules/nf-core/bcftools/query/environment.yml index 4f9661ca..d8c4f4e4 100644 --- a/modules/nf-core/bcftools/query/environment.yml +++ b/modules/nf-core/bcftools/query/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf index e9e73a6a..58019f4d 100644 --- a/modules/nf-core/bcftools/query/main.nf +++ b/modules/nf-core/bcftools/query/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_QUERY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/query/tests/main.nf.test b/modules/nf-core/bcftools/query/tests/main.nf.test index e9ea5a9d..39e67b35 100644 --- a/modules/nf-core/bcftools/query/tests/main.nf.test +++ b/modules/nf-core/bcftools/query/tests/main.nf.test @@ -18,8 +18,8 @@ nextflow_process { """ input[0] = [ [ id:'out' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) ] input[1] = [] input[2] = [] @@ -47,11 +47,11 @@ nextflow_process { """ input[0] = [ [ id:'out' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) ] - input[1] = file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['illumina']['test2_vcf_targets_tsv_gz'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz', checkIfExists: true) input[3] = [] """ } @@ -76,8 +76,8 @@ nextflow_process { """ input[0] = [ [ id:'out' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) ] input[1] = [] input[2] = [] diff --git a/modules/nf-core/bcftools/query/tests/main.nf.test.snap b/modules/nf-core/bcftools/query/tests/main.nf.test.snap index a19f2053..3ead1f2c 100644 --- a/modules/nf-core/bcftools/query/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/query/tests/main.nf.test.snap @@ -10,19 +10,27 @@ ] ], [ - "versions.yml:md5,b40206d5437ce4b044d15c47ddd93d8e" + "versions.yml:md5,3d93ea9cd5d314743254618b49e4bd16" ] ], - "timestamp": "2023-11-29T14:21:05.191946862" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T15:15:44.916249758" }, "sarscov2 - [vcf, tbi], [], [], [] - stub": { "content": [ "out.txt", [ - "versions.yml:md5,b40206d5437ce4b044d15c47ddd93d8e" + "versions.yml:md5,3d93ea9cd5d314743254618b49e4bd16" ] ], - "timestamp": "2023-11-29T14:21:11.169603542" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T15:15:49.932359271" }, "sarscov2 - [vcf, tbi], [], [], []": { "content": [ @@ -35,9 +43,13 @@ ] ], [ - "versions.yml:md5,b40206d5437ce4b044d15c47ddd93d8e" + "versions.yml:md5,3d93ea9cd5d314743254618b49e4bd16" ] ], - "timestamp": "2023-11-29T14:20:59.335041418" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T15:15:39.930697926" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/reheader/bcftools-reheader.diff b/modules/nf-core/bcftools/reheader/bcftools-reheader.diff deleted file mode 100644 index 57637baa..00000000 --- a/modules/nf-core/bcftools/reheader/bcftools-reheader.diff +++ /dev/null @@ -1,19 +0,0 @@ -Changes in module 'nf-core/bcftools/reheader' ---- modules/nf-core/bcftools/reheader/main.nf -+++ modules/nf-core/bcftools/reheader/main.nf -@@ -31,10 +31,13 @@ - args2.contains("--output-type v") || args2.contains("-Ov") ? "vcf" : - "vcf" - """ -+ echo ${meta.sample} > sample.txt -+ - bcftools \\ - reheader \\ - $update_sequences \\ - $new_header \\ -+ --samples sample.txt \\ - $args \\ - --threads $task.cpus \\ - $vcf \\ - -************************************************************ diff --git a/modules/nf-core/bcftools/reheader/environment.yml b/modules/nf-core/bcftools/reheader/environment.yml index aab0dc92..48fd72c9 100644 --- a/modules/nf-core/bcftools/reheader/environment.yml +++ b/modules/nf-core/bcftools/reheader/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/reheader/main.nf b/modules/nf-core/bcftools/reheader/main.nf index 82527167..9cf6d0d3 100644 --- a/modules/nf-core/bcftools/reheader/main.nf +++ b/modules/nf-core/bcftools/reheader/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_REHEADER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcf), path(header), path(samples) @@ -13,6 +13,7 @@ process BCFTOOLS_REHEADER { output: tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.{csi,tbi}") , emit: index, optional: true path "versions.yml" , emit: versions when: @@ -59,8 +60,16 @@ process BCFTOOLS_REHEADER { args2.contains("--output-type z") || args2.contains("-Oz") ? "vcf.gz" : args2.contains("--output-type v") || args2.contains("-Ov") ? "vcf" : "vcf" + def index = args2.contains("--write-index=tbi") || args2.contains("-W=tbi") ? "tbi" : + args2.contains("--write-index=csi") || args2.contains("-W=csi") ? "csi" : + args2.contains("--write-index") || args2.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + """ - touch ${prefix}.${extension} + ${create_cmd} ${prefix}.${extension} + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/reheader/meta.yml b/modules/nf-core/bcftools/reheader/meta.yml index 690d4ead..d903cc0f 100644 --- a/modules/nf-core/bcftools/reheader/meta.yml +++ b/modules/nf-core/bcftools/reheader/meta.yml @@ -53,6 +53,10 @@ output: type: file description: VCF with updated header, bgzipped per default pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - index: + type: file + description: Index of VCF with updated header + pattern: "*.{csi,tbi}" authors: - "@bjohnnyd" - "@jemten" diff --git a/modules/nf-core/bcftools/reheader/tests/main.nf.test b/modules/nf-core/bcftools/reheader/tests/main.nf.test index f3200cb3..96c1b7b0 100644 --- a/modules/nf-core/bcftools/reheader/tests/main.nf.test +++ b/modules/nf-core/bcftools/reheader/tests/main.nf.test @@ -17,13 +17,13 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [], [] ] - input[1] = [ + input[1] = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] """ } @@ -47,13 +47,13 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [], [] ] - input[1] = [ + input[1] = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] """ } @@ -68,6 +68,111 @@ nextflow_process { } + test("sarscov2 - [vcf, [], []], fai - vcf.gz output - index") { + + config "./vcf_gz_index.config" + when { + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.index[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index") { + + config "./vcf_gz_index_csi.config" + when { + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.index[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index") { + + config "./vcf_gz_index_tbi.config" + when { + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.index[0][1].endsWith(".tbi") } + ) + } + + } + test("sarscov2 - [vcf, [], []], fai - bcf output") { config "./bcf.config" @@ -77,13 +182,13 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [], [] ] - input[1] = [ + input[1] = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] """ } @@ -107,11 +212,11 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), [] ] - input[1] = [ + input[1] = [ [ id:'genome' ], // meta map [] ] @@ -137,15 +242,15 @@ nextflow_process { """ ch_no_samples = Channel.of([ [ id:'test', single_end:false ], - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [] ]) ch_samples = Channel.of(["samples.txt", "new_name"]) .collectFile(newLine:true) input[0] = ch_no_samples.combine(ch_samples) - input[1] = [ + input[1] = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] """ } @@ -170,13 +275,13 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [], [] ] - input[1] = [ + input[1] = [ [ id:'genome' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] """ } @@ -193,5 +298,97 @@ nextflow_process { } } + test("sarscov2 - [vcf, [], []], fai - vcf.gz output - index -stub") { + + options "-stub" + config "./vcf_gz_index.config" + when { + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index -stub") { + + options "-stub" + config "./vcf_gz_index_csi.config" + when { + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index -stub") { + + options "-stub" + config "./vcf_gz_index_tbi.config" + when { + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } } diff --git a/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap b/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap index 112736a1..87a3654a 100644 --- a/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/reheader/tests/main.nf.test.snap @@ -1,4 +1,140 @@ { + "sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T10:09:05.955833763" + }, + "sarscov2 - [vcf, [], []], fai - vcf.gz output - index -stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ], + "index": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T09:52:41.444952182" + }, + "sarscov2 - [vcf, [], []], fai - vcf.gz output - tbi index -stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ], + "index": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T09:53:04.314827944" + }, "sarscov2 - [vcf, [], []], fai - vcf output": { "content": [ { @@ -12,7 +148,13 @@ ] ], "1": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + + ], + "2": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ], + "index": [ + ], "vcf": [ [ @@ -24,11 +166,15 @@ ] ], "versions": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" ] } ], - "timestamp": "2023-11-29T13:05:44.058376693" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T09:50:41.983008108" }, "sarscov2 - [vcf, [], []], fai - bcf output": { "content": [ @@ -39,11 +185,17 @@ "id": "test", "single_end": false }, - "tested.bcf.gz:md5,c31d9afd8614832c2a46d9a55682c97a" + "tested.bcf.gz:md5,c8a304c8d2892039201154153c8cd536" ] ], "1": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + + ], + "2": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ], + "index": [ + ], "vcf": [ [ @@ -51,15 +203,19 @@ "id": "test", "single_end": false }, - "tested.bcf.gz:md5,c31d9afd8614832c2a46d9a55682c97a" + "tested.bcf.gz:md5,c8a304c8d2892039201154153c8cd536" ] ], "versions": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" ] } ], - "timestamp": "2023-11-29T13:06:03.793372514" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T09:51:43.072513252" }, "sarscov2 - [vcf, [], []], fai - vcf.gz output": { "content": [ @@ -70,11 +226,17 @@ "id": "test", "single_end": false }, - "tested.vcf.gz:md5,a1e45fe6d2b386fc2611766e5d2937ee" + "tested.vcf.gz:md5,8e722884ffb75155212a3fc053918766" ] ], "1": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + + ], + "2": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ], + "index": [ + ], "vcf": [ [ @@ -82,24 +244,145 @@ "id": "test", "single_end": false }, - "tested.vcf.gz:md5,a1e45fe6d2b386fc2611766e5d2937ee" + "tested.vcf.gz:md5,8e722884ffb75155212a3fc053918766" ] ], "versions": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" ] } ], - "timestamp": "2023-11-29T13:05:53.954090441" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T09:50:53.055630152" + }, + "sarscov2 - [vcf, [], []], fai - vcf.gz output - index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T10:08:37.999924355" + }, + "sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index -stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ], + "index": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T09:52:52.512269206" }, "sarscov2 - [vcf, [], []], fai - stub": { "content": [ "tested.vcf", [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" ] ], - "timestamp": "2023-11-29T13:06:33.549685303" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T15:16:36.337112514" + }, + "sarscov2 - [vcf, [], []], fai - vcf.gz output - csi index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T10:08:55.434831174" }, "sarscov2 - [vcf, [], samples], fai": { "content": [ @@ -114,7 +397,13 @@ ] ], "1": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + + ], + "2": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ], + "index": [ + ], "vcf": [ [ @@ -126,11 +415,15 @@ ] ], "versions": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" ] } ], - "timestamp": "2023-11-29T13:06:23.474745156" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T09:52:12.216002665" }, "sarscov2 - [vcf, header, []], []": { "content": [ @@ -145,7 +438,13 @@ ] ], "1": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + + ], + "2": [ + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" + ], + "index": [ + ], "vcf": [ [ @@ -157,10 +456,14 @@ ] ], "versions": [ - "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce" + "versions.yml:md5,486e3d4ebc1dbf5c0a4dfaebae12ea34" ] } ], - "timestamp": "2023-11-29T13:06:13.841648691" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-09-03T09:51:54.062386022" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/reheader/tests/vcf_gz_index.config b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index.config new file mode 100644 index 00000000..1e050ec7 --- /dev/null +++ b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args2 = "--output-type z --write-index --no-version" +} diff --git a/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..536e4b42 --- /dev/null +++ b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args2 = "--output-type z --write-index=csi --no-version" +} diff --git a/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..91a80db7 --- /dev/null +++ b/modules/nf-core/bcftools/reheader/tests/vcf_gz_index_tbi.config @@ -0,0 +1,5 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args2 = "--output-type z --write-index=tbi --no-version" + +} diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml index 89cf911d..2295ecfd 100644 --- a/modules/nf-core/bcftools/sort/environment.yml +++ b/modules/nf-core/bcftools/sort/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index c982944c..7d4c9b8e 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -4,15 +4,17 @@ process BCFTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcf) output: - tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}") , emit: vcf - path "versions.yml" , emit: versions + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -49,9 +51,16 @@ process BCFTOOLS_SORT { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" """ - touch ${prefix}.${extension} + ${create_cmd} ${prefix}.${extension} + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/sort/meta.yml b/modules/nf-core/bcftools/sort/meta.yml index 84747c6d..dfbddcba 100644 --- a/modules/nf-core/bcftools/sort/meta.yml +++ b/modules/nf-core/bcftools/sort/meta.yml @@ -36,6 +36,14 @@ output: type: file description: Sorted VCF file pattern: "*.{vcf.gz}" + - csi: + type: file + description: Default VCF file index + pattern: "*.csi" + - tbi: + type: file + description: Alternative VCF file index + pattern: "*.tbi" authors: - "@Gwennid" maintainers: diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test b/modules/nf-core/bcftools/sort/tests/main.nf.test new file mode 100644 index 00000000..b9bdd76a --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/main.nf.test @@ -0,0 +1,222 @@ +nextflow_process { + + name "Test Process BCFTOOLS_SORT" + script "../main.nf" + process "BCFTOOLS_SORT" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/sort" + + test("sarscov2 - vcf") { + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match("vcf") } + ) + } + + } + + test("sarscov2 - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + test("sarscov2 - vcf - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test.snap b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap new file mode 100644 index 00000000..f38272cb --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap @@ -0,0 +1,350 @@ +{ + "sarscov2 - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:06:05.201680777" + }, + "vcf": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "versions": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:04:43.889971134" + }, + "sarscov2 - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:04:55.385964497" + }, + "sarscov2 - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:05:06.662818922" + }, + "sarscov2 - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ], + "csi": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:05:40.012912381" + }, + "sarscov2 - vcf_gz_index_csi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ], + "csi": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:05:52.405673587" + }, + "sarscov2 - vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:05:29.117946461" + }, + "sarscov2 - vcf_gz_index_tbi": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + + ], + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:05:17.217274984" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/sort/tests/tags.yml b/modules/nf-core/bcftools/sort/tests/tags.yml new file mode 100644 index 00000000..6e9520dd --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/sort: + - "modules/nf-core/bcftools/sort/**" diff --git a/modules/nf-core/bcftools/sort/tests/vcf_gz_index.config b/modules/nf-core/bcftools/sort/tests/vcf_gz_index.config new file mode 100644 index 00000000..aacd1346 --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index" +} diff --git a/modules/nf-core/bcftools/sort/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/sort/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..640eb0ba --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi" +} diff --git a/modules/nf-core/bcftools/sort/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/sort/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..589a50c6 --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi" +} diff --git a/modules/nf-core/bcftools/stats/environment.yml b/modules/nf-core/bcftools/stats/environment.yml index 1a969528..128fe204 100644 --- a/modules/nf-core/bcftools/stats/environment.yml +++ b/modules/nf-core/bcftools/stats/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf index ffa1df64..20e5da77 100644 --- a/modules/nf-core/bcftools/stats/main.nf +++ b/modules/nf-core/bcftools/stats/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/stats/tests/main.nf.test b/modules/nf-core/bcftools/stats/tests/main.nf.test new file mode 100644 index 00000000..be618b0b --- /dev/null +++ b/modules/nf-core/bcftools/stats/tests/main.nf.test @@ -0,0 +1,182 @@ +nextflow_process { + + name "Test Process BCFTOOLS_STATS" + script "../main.nf" + process "BCFTOOLS_STATS" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/stats" + + test("sarscov2 - vcf_gz") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + []] + input[1] = [ [], [] ] + input[2] = [ [], [] ] + input[3] = [ [], [] ] + input[4] = [ [], [] ] + input[5] = [ [], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match("versions") }, + { assert snapshot(file(process.out.stats.get(0).get(1)).readLines()[0..5]).match() }, + ) + } + + } + + test("sarscov2 - vcf_gz - regions") { + + when { + process { + """ + input[0] = [ [ id:'regions_test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)] + input[1] = [ [id:'regions_test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) ] + input[2] = [ [], [] ] + input[3] = [ [], [] ] + input[4] = [ [], [] ] + input[5] = [ [], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match("regions_versions") }, + { assert snapshot(file(process.out.stats.get(0).get(1)).readLines()[0..5]).match() }, + ) + } + + } + + test("sarscov2 - vcf_gz - targets") { + + when { + process { + """ + input[0] = [ [ id:'targets_test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] ] + input[1] = [ [], [] ] + input[2] = [ [id:'targets_test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz', checkIfExists: true) + ] + input[3] = [ [], [] ] + input[4] = [ [], [] ] + input[5] = [ [], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match("targets_versions") }, + { assert snapshot(file(process.out.stats.get(0).get(1)).readLines()[0..5]).match() }, + ) + } + + } + + test("sarscov2 - vcf_gz - exons") { + + when { + process { + """ + input[0] = [ [ id:'exon_test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] ] + input[1] = [ [], [] ] + input[2] = [ [], [] ] + input[3] = [ [], [] ] + input[4] = [ [id: "exon_test"], + file(params.modules_testdata_base_path + 'delete_me/bcftools/stats/exons.tsv.gz', checkIfExists: true) ] + input[5] = [ [], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match("exon_versions") }, + { assert snapshot(file(process.out.stats.get(0).get(1)).readLines()[0..5]).match() }, + ) + } + + } + + test("sarscov2 - vcf_gz - reference") { + + when { + process { + """ + input[0] = [ [ id:'ref_test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [] ] + input[1] = [ [], [] ] + input[2] = [ [], [] ] + input[3] = [ [], [] ] + input[4] = [ [], [] ] + input[5] = [ [id: 'ref_test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match("ref_versions") }, + { assert snapshot(file(process.out.stats.get(0).get(1)).readLines()[0..5]).match() }, + ) + } + + } + + + test("sarscov2 - vcf_gz - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + []] + input[1] = [ [], [] ] + input[2] = [ [], [] ] + input[3] = [ [], [] ] + input[4] = [ [], [] ] + input[5] = [ [], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/stats/tests/main.nf.test.snap b/modules/nf-core/bcftools/stats/tests/main.nf.test.snap new file mode 100644 index 00000000..cd8cff6d --- /dev/null +++ b/modules/nf-core/bcftools/stats/tests/main.nf.test.snap @@ -0,0 +1,180 @@ +{ + "sarscov2 - vcf_gz - reference": { + "content": [ + [ + "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.", + "# The command line was:\tbcftools stats --fasta-ref genome.fasta test.vcf.gz", + "#", + "# Definition of sets:", + "# ID\t[2]id\t[3]tab-separated file names", + "ID\t0\ttest.vcf.gz" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:14:35.506777837" + }, + "sarscov2 - vcf_gz - exons": { + "content": [ + [ + "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.", + "# The command line was:\tbcftools stats --exons exons.tsv.gz test.vcf.gz", + "#", + "# Definition of sets:", + "# ID\t[2]id\t[3]tab-separated file names", + "ID\t0\ttest.vcf.gz" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:14:30.57486244" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:16:27.637515559" + }, + "sarscov2 - vcf_gz - targets": { + "content": [ + [ + "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.", + "# The command line was:\tbcftools stats --targets-file test2.targets.tsv.gz test.vcf.gz", + "#", + "# Definition of sets:", + "# ID\t[2]id\t[3]tab-separated file names", + "ID\t0\ttest.vcf.gz" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:14:25.732997442" + }, + "regions_versions": { + "content": [ + [ + "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:16:32.559884458" + }, + "targets_versions": { + "content": [ + [ + "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:16:37.512009805" + }, + "sarscov2 - vcf_gz - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a" + ], + "stats": [ + [ + { + "id": "test" + }, + "test.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-03T11:57:09.614976125" + }, + "exon_versions": { + "content": [ + [ + "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:16:42.347397266" + }, + "ref_versions": { + "content": [ + [ + "versions.yml:md5,17cdf9d1ad31f6b1f5935dfcc9fe7b9a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:16:47.26823622" + }, + "sarscov2 - vcf_gz": { + "content": [ + [ + "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.", + "# The command line was:\tbcftools stats test.vcf.gz", + "#", + "# Definition of sets:", + "# ID\t[2]id\t[3]tab-separated file names", + "ID\t0\ttest.vcf.gz" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:16:27.670416598" + }, + "sarscov2 - vcf_gz - regions": { + "content": [ + [ + "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.", + "# The command line was:\tbcftools stats --regions-file test3.vcf.gz test.vcf.gz", + "#", + "# Definition of sets:", + "# ID\t[2]id\t[3]tab-separated file names", + "ID\t0\ttest.vcf.gz" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-31T18:14:20.759094062" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/stats/tests/tags.yml b/modules/nf-core/bcftools/stats/tests/tags.yml new file mode 100644 index 00000000..53c12d92 --- /dev/null +++ b/modules/nf-core/bcftools/stats/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/stats: + - "modules/nf-core/bcftools/stats/**" diff --git a/modules/nf-core/ensemblvep/download/ensemblvep-download.diff b/modules/nf-core/ensemblvep/download/ensemblvep-download.diff deleted file mode 100644 index 954d28c3..00000000 --- a/modules/nf-core/ensemblvep/download/ensemblvep-download.diff +++ /dev/null @@ -1,25 +0,0 @@ -Changes in module 'nf-core/ensemblvep/download' ---- modules/nf-core/ensemblvep/download/main.nf -+++ modules/nf-core/ensemblvep/download/main.nf -@@ -4,8 +4,8 @@ - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : -- 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }" -+ 'https://depot.galaxyproject.org/singularity/ensembl-vep:105.0--pl5321h4a94de4_1' : -+ 'biocontainers/ensembl-vep:105.0--pl5321h4a94de4_1' }" - - input: - tuple val(meta), val(assembly), val(species), val(cache_version) - ---- modules/nf-core/ensemblvep/download/environment.yml -+++ modules/nf-core/ensemblvep/download/environment.yml -@@ -4,4 +4,4 @@ - - bioconda - - defaults - dependencies: -- - bioconda::ensembl-vep=110.0 -+ - bioconda::ensembl-vep=105.0 - -************************************************************ diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml index adba76e8..91564cce 100644 --- a/modules/nf-core/ensemblvep/download/environment.yml +++ b/modules/nf-core/ensemblvep/download/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::ensembl-vep=105.0 + - bioconda::ensembl-vep=112.0 diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf index f6ed5872..555c3c66 100644 --- a/modules/nf-core/ensemblvep/download/main.nf +++ b/modules/nf-core/ensemblvep/download/main.nf @@ -4,24 +4,25 @@ process ENSEMBLVEP_DOWNLOAD { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:105.0--pl5321h4a94de4_1' : - 'biocontainers/ensembl-vep:105.0--pl5321h4a94de4_1' }" + 'https://depot.galaxyproject.org/singularity/ensembl-vep:112.0--pl5321h2a3209d_0' : + 'biocontainers/ensembl-vep:112.0--pl5321h2a3209d_0' }" input: tuple val(meta), val(assembly), val(species), val(cache_version) output: - tuple val(meta), path("vep_cache"), emit: cache - path "versions.yml" , emit: versions + tuple val(meta), path(prefix), emit: cache + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: 'vep_cache' """ vep_install \\ - --CACHEDIR vep_cache \\ + --CACHEDIR $prefix \\ --SPECIES $species \\ --ASSEMBLY $assembly \\ --CACHE_VERSION $cache_version \\ @@ -34,8 +35,9 @@ process ENSEMBLVEP_DOWNLOAD { """ stub: + prefix = task.ext.prefix ?: 'vep_cache' """ - mkdir vep_cache + mkdir $prefix cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test b/modules/nf-core/ensemblvep/download/tests/main.nf.test new file mode 100644 index 00000000..ac41cc3f --- /dev/null +++ b/modules/nf-core/ensemblvep/download/tests/main.nf.test @@ -0,0 +1,60 @@ +nextflow_process { + + name "Test Process ENSEMBLVEP_DOWNLOAD" + script "../main.nf" + process "ENSEMBLVEP_DOWNLOAD" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "ensemblvep" + tag "ensemblvep/download" + + test("celegans - download") { + + when { + process { + """ + input[0] = Channel.of([ + [id:"112_WBcel235"], + params.vep_genome, + params.vep_species, + params.vep_cache_version + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("celegans - download - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [id:"112_WBcel235"], + params.vep_genome, + params.vep_species, + params.vep_cache_version + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap new file mode 100644 index 00000000..9e303c54 --- /dev/null +++ b/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap @@ -0,0 +1,322 @@ +{ + "celegans - download": { + "content": [ + { + "0": [ + [ + { + "id": "112_WBcel235" + }, + [ + [ + [ + [ + "1-1000000.gz:md5,c7df2324c613caafe70024bb156b077c", + "10000001-11000000.gz:md5,baee612beb1fc7b931d1b4c34df9a366", + "1000001-2000000.gz:md5,4fefec2bbbcdc22022ba22e2b36fe118", + "11000001-12000000.gz:md5,e06df8391870440be75a3a0fed05ad29", + "12000001-13000000.gz:md5,3abd252ef8e0c79d7be07dfe7503c38b", + "13000001-14000000.gz:md5,9b20be645c68c1ef16f0aaadc9d1899d", + "14000001-15000000.gz:md5,c80817caa2a893c8059ad9a66e1c2c1a", + 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"versions": [ + "versions.yml:md5,e32852e9cba2a298b7518ce610011b14" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-02T13:19:08.690863" + }, + "celegans - download - stub": { + "content": [ + { + "0": [ + [ + { + "id": "112_WBcel235" + }, + [ + + ] + ] + ], + "1": [ + "versions.yml:md5,e32852e9cba2a298b7518ce610011b14" + ], + "cache": [ + [ + { + "id": "112_WBcel235" + }, + [ + + ] + ] + ], + "versions": [ + "versions.yml:md5,e32852e9cba2a298b7518ce610011b14" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-02T13:19:23.308683" + } +} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/download/tests/nextflow.config b/modules/nf-core/ensemblvep/download/tests/nextflow.config new file mode 100644 index 00000000..9aa48164 --- /dev/null +++ b/modules/nf-core/ensemblvep/download/tests/nextflow.config @@ -0,0 +1,12 @@ +params { + vep_cache_version = "112" + vep_genome = "WBcel235" + vep_species = "caenorhabditis_elegans" +} + +process { + withName: ENSEMBLVEP_DOWNLOAD { + ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' + ext.prefix = { "${params.vep_cache_version}_${params.vep_genome}" } + } +} diff --git a/modules/nf-core/ensemblvep/download/tests/tags.yml b/modules/nf-core/ensemblvep/download/tests/tags.yml new file mode 100644 index 00000000..26671f3d --- /dev/null +++ b/modules/nf-core/ensemblvep/download/tests/tags.yml @@ -0,0 +1,2 @@ +ensemblvep/download: + - "modules/nf-core/ensemblvep/download/**" diff --git a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff deleted file mode 100644 index 63309f0b..00000000 --- a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff +++ /dev/null @@ -1,38 +0,0 @@ -Changes in module 'nf-core/ensemblvep/vep' ---- modules/nf-core/ensemblvep/vep/main.nf -+++ modules/nf-core/ensemblvep/vep/main.nf -@@ -2,10 +2,10 @@ - tag "$meta.id" - label 'process_medium' - -- conda "bioconda::ensembl-vep=109.3" -+ conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'https://depot.galaxyproject.org/singularity/ensembl-vep:109.3--pl5321h2a3209d_1' : -- 'biocontainers/ensembl-vep:109.3--pl5321h2a3209d_1' }" -+ 'https://depot.galaxyproject.org/singularity/ensembl-vep:105.0--pl5321h4a94de4_1' : -+ 'biocontainers/ensembl-vep:105.0--pl5321h4a94de4_1' }" - - input: - tuple val(meta), path(vcf), path(custom_extra_files) -@@ -48,7 +48,6 @@ - --fork $task.cpus \\ - --stats_file ${prefix}.summary.html \\ - -- - cat <<-END_VERSIONS > versions.yml - "${task.process}": - ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') - ---- /dev/null -+++ modules/nf-core/ensemblvep/vep/environment.yml -@@ -0,0 +1,7 @@ -+name: ensemblvep_download -+channels: -+ - conda-forge -+ - bioconda -+ - defaults -+dependencies: -+ - bioconda::ensembl-vep=105.0 - -************************************************************ diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml index adba76e8..3eae4fb1 100644 --- a/modules/nf-core/ensemblvep/vep/environment.yml +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -1,7 +1,7 @@ -name: ensemblvep_download +name: ensemblvep_vep channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::ensembl-vep=105.0 + - bioconda::ensembl-vep=112.0 diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index 65fbd53d..5f33265b 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -4,8 +4,8 @@ process ENSEMBLVEP_VEP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:105.0--pl5321h4a94de4_1' : - 'biocontainers/ensembl-vep:105.0--pl5321h4a94de4_1' }" + 'https://depot.galaxyproject.org/singularity/ensembl-vep:112.0--pl5321h2a3209d_0' : + 'biocontainers/ensembl-vep:112.0--pl5321h2a3209d_0' }" input: tuple val(meta), path(vcf), path(custom_extra_files) @@ -20,7 +20,7 @@ process ENSEMBLVEP_VEP { tuple val(meta), path("*.vcf.gz") , optional:true, emit: vcf tuple val(meta), path("*.tab.gz") , optional:true, emit: tab tuple val(meta), path("*.json.gz") , optional:true, emit: json - path "*.summary.html" , emit: report + path "*.html" , optional:true, emit: report path "versions.yml" , emit: versions when: @@ -45,8 +45,8 @@ process ENSEMBLVEP_VEP { --cache \\ --cache_version $cache_version \\ --dir_cache $dir_cache \\ - --fork $task.cpus \\ - --stats_file ${prefix}.summary.html \\ + --fork $task.cpus + cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -57,10 +57,10 @@ process ENSEMBLVEP_VEP { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf.gz - touch ${prefix}.tab.gz - touch ${prefix}.json.gz - touch ${prefix}.summary.html + echo "" | gzip > ${prefix}.vcf.gz + echo "" | gzip > ${prefix}.tab.gz + echo "" | gzip > ${prefix}.json.gz + touch ${prefix}_summary.html cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml index 7783847d..d8ff8d14 100644 --- a/modules/nf-core/ensemblvep/vep/meta.yml +++ b/modules/nf-core/ensemblvep/vep/meta.yml @@ -1,4 +1,4 @@ -name: ENSEMBLVEP_VEP +name: ensemblvep_vep description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`. keywords: - annotation @@ -86,3 +86,7 @@ authors: - "@maxulysse" - "@matthdsm" - "@nvnieuwk" +maintainers: + - "@maxulysse" + - "@matthdsm" + - "@nvnieuwk" diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test new file mode 100644 index 00000000..e68fff3c --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test @@ -0,0 +1,114 @@ +nextflow_process { + + name "Test Process ENSEMBLVEP_VEP" + script "../main.nf" + process "ENSEMBLVEP_VEP" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "ensemblvep" + tag "ensemblvep/vep" + tag "ensemblvep/download" + + test("test_ensemblvep_vep_fasta_vcf") { + config "./vcf.config" + + setup { + run("ENSEMBLVEP_DOWNLOAD") { + script "../../download/main.nf" + + process { + """ + input[0] = Channel.of([ + [id:"112_WBcel235"], + params.vep_genome, + params.vep_species, + params.vep_cache_version + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] + ]) + input[1] = params.vep_genome + input[2] = params.vep_species + input[3] = params.vep_cache_version + input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] } + input[5] = Channel.value([ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[6] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") } + ) + } + + } + + test("test_ensemblvep_vep_fasta_tab_gz") { + config "./tab.gz.config" + + setup { + run("ENSEMBLVEP_DOWNLOAD") { + script "../../download/main.nf" + + process { + """ + input[0] = Channel.of([ + [id:"112_WBcel235"], + params.vep_genome, + params.vep_species, + params.vep_cache_version + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] + ]) + input[1] = params.vep_genome + input[2] = params.vep_species + input[3] = params.vep_cache_version + input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] } + input[5] = Channel.value([ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[6] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + { assert path(process.out.tab.get(0).get(1)).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v112.0") } + ) + } + } +} diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap new file mode 100644 index 00000000..1c4c0e4e --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap @@ -0,0 +1,26 @@ +{ + "test_ensemblvep_vep_fasta_tab_gz": { + "content": [ + [ + "versions.yml:md5,d06f1eb60f534489026d682eb3aa5559" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-02T10:15:18.228927" + }, + "test_ensemblvep_vep_fasta_vcf": { + "content": [ + [ + "versions.yml:md5,d06f1eb60f534489026d682eb3aa5559" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-02T10:14:50.193861" + } +} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/vep/tests/nextflow.config b/modules/nf-core/ensemblvep/vep/tests/nextflow.config new file mode 100644 index 00000000..9aa48164 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/nextflow.config @@ -0,0 +1,12 @@ +params { + vep_cache_version = "112" + vep_genome = "WBcel235" + vep_species = "caenorhabditis_elegans" +} + +process { + withName: ENSEMBLVEP_DOWNLOAD { + ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' + ext.prefix = { "${params.vep_cache_version}_${params.vep_genome}" } + } +} diff --git a/modules/nf-core/ensemblvep/vep/tests/tab.gz.config b/modules/nf-core/ensemblvep/vep/tests/tab.gz.config new file mode 100644 index 00000000..40eb03e5 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/tab.gz.config @@ -0,0 +1,5 @@ +process { + withName: ENSEMBLVEP_VEP { + ext.args = '--tab --compress_output bgzip' + } +} diff --git a/modules/nf-core/ensemblvep/vep/tests/tags.yml b/modules/nf-core/ensemblvep/vep/tests/tags.yml new file mode 100644 index 00000000..4aa4aa45 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/tags.yml @@ -0,0 +1,2 @@ +ensemblvep/vep: + - "modules/nf-core/ensemblvep/vep/**" diff --git a/modules/nf-core/ensemblvep/vep/tests/vcf.config b/modules/nf-core/ensemblvep/vep/tests/vcf.config new file mode 100644 index 00000000..ad8955a3 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/vcf.config @@ -0,0 +1,5 @@ +process { + withName: ENSEMBLVEP_VEP { + ext.args = '--vcf' + } +} diff --git a/modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff b/modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff deleted file mode 100644 index 2369ffbc..00000000 --- a/modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff +++ /dev/null @@ -1,13 +0,0 @@ -Changes in module 'nf-core/gatk4/genotypegvcfs' ---- modules/nf-core/gatk4/genotypegvcfs/main.nf -+++ modules/nf-core/gatk4/genotypegvcfs/main.nf -@@ -1,6 +1,6 @@ - process GATK4_GENOTYPEGVCFS { - tag "$meta.id" -- label 'process_high' -+ label 'process_single' - - conda "bioconda::gatk4=4.4.0.0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - -************************************************************ diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index 3a9fbb4e..f180f749 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -8,12 +8,12 @@ process GATK4_GENOTYPEGVCFS { 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: - tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index) - path fasta - path fai - path dict - path dbsnp - path dbsnp_tbi + tuple val(meta), path(input), path(gvcf_index), path(intervals), path(intervals_index) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) + tuple val(meta5), path(dbsnp) + tuple val(meta6), path(dbsnp_tbi) output: tuple val(meta), path("*.vcf.gz"), emit: vcf @@ -26,7 +26,7 @@ process GATK4_GENOTYPEGVCFS { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def gvcf_command = gvcf.name.endsWith(".vcf") || gvcf.name.endsWith(".vcf.gz") ? "$gvcf" : "gendb://$gvcf" + def input_command = input.name.endsWith(".vcf") || input.name.endsWith(".vcf.gz") ? "$input" : "gendb://$input" def dbsnp_command = dbsnp ? "--dbsnp $dbsnp" : "" def interval_command = intervals ? "--intervals $intervals" : "" @@ -39,7 +39,7 @@ process GATK4_GENOTYPEGVCFS { """ gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ GenotypeGVCFs \\ - --variant $gvcf_command \\ + --variant $input_command \\ --output ${prefix}.vcf.gz \\ --reference $fasta \\ $interval_command \\ @@ -57,7 +57,7 @@ process GATK4_GENOTYPEGVCFS { def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf.gz + echo | gzip > ${prefix}.vcf.gz touch ${prefix}.vcf.gz.tbi cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/gatk4/genotypegvcfs/meta.yml b/modules/nf-core/gatk4/genotypegvcfs/meta.yml index 8f1e377e..eb704364 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/meta.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/meta.yml @@ -20,10 +20,10 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - gvcf: + - input: type: file description: | - gVCF(.gz) file or to a GenomicsDB + gVCF(.gz) file or a GenomicsDB pattern: "*.{vcf,vcf.gz}" - gvcf_index: type: file @@ -36,22 +36,47 @@ input: - intervals_index: type: file description: Interval index file (optional) + - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] - fasta: type: file description: Reference fasta file pattern: "*.fasta" + - meta3: + type: map + description: | + Groovy Map containing fai information + e.g. [ id:'test' ] - fai: type: file description: Reference fasta index file pattern: "*.fai" + - meta4: + type: map + description: | + Groovy Map containing dict information + e.g. [ id:'test' ] - dict: type: file description: Reference fasta sequence dict file pattern: "*.dict" + - meta5: + type: map + description: | + Groovy Map containing dbsnp information + e.g. [ id:'test' ] - dbsnp: type: file description: dbSNP VCF file pattern: "*.vcf.gz" + - meta6: + type: map + description: | + Groovy Map containing dbsnp tbi information + e.g. [ id:'test' ] - dbsnp_tbi: type: file description: dbSNP VCF index file diff --git a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test new file mode 100644 index 00000000..25bc2d38 --- /dev/null +++ b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test @@ -0,0 +1,285 @@ +nextflow_process { + + name "Test Process GATK4_GENOTYPEGVCFS" + script "../main.nf" + process "GATK4_GENOTYPEGVCFS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/genotypegvcfs" + tag "untar" + + setup { + run("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = [ + [id:"test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz', checkIfExists: true) + ] + """ + } + } + } + + test("homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], []") { + + when { + process { + """ + input[0] = [ + [id:"test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true), + [], + [] + ] + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] }, + process.out.tbi.collect { [it[0], file(it[1]).name] }, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [gvcf_gz, tbi, [], []], fasta, fai, dict, dbsnp, dbsnp_tbi") { + + when { + process { + """ + input[0] = [ + [id:"test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + [], + [] + ] + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [ + [id:"dbsnp"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists:true) + ] + input[5] = [ + [id:"dbsnp"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists:true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] }, + process.out.tbi.collect { [it[0], file(it[1]).name] }, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [gvcf_gz, tbi, bed, []], fasta, fai, dict, [], []") { + + when { + process { + """ + input[0] = [ + [id:"test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists:true), + [] + ] + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] }, + process.out.tbi.collect { [it[0], file(it[1]).name] }, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [gendb, [], [], []], fasta, fai, dict, [], []") { + + when { + process { + """ + input[0] = UNTAR.out.untar.map { meta, gendb -> [ meta, gendb, [], [], []] } + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] }, + process.out.tbi.collect { [it[0], file(it[1]).name] }, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [gendb, bed, [], []], fasta, fai, dict, [], []") { + + when { + process { + """ + input[0] = UNTAR.out.untar.map { meta, gendb -> + [ + meta, + gendb, + [], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists:true), + [] + ] + } + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { [it[0], path(it[1]).vcf.variantsMD5] }, + process.out.tbi.collect { [it[0], file(it[1]).name] }, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], [] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [id:"test"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true), + [], + [] + ] + input[1] = [ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true) + ] + input[2] = [ + [id:"fai"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true) + ] + input[3] = [ + [id:"dict"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists:true) + ] + input[4] = [[],[]] + input[5] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap new file mode 100644 index 00000000..1621618e --- /dev/null +++ b/modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap @@ -0,0 +1,191 @@ +{ + "homo_sapiens - [gendb, [], [], []], fasta, fai, dict, [], []": { + "content": [ + [ + [ + { + "id": "test" + }, + "1ab95fbc5ec55b208f3001572bec54fa" + ] + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T14:27:24.926097884" + }, + "homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], []": { + "content": [ + [ + [ + { + "id": "test" + }, + "1ab95fbc5ec55b208f3001572bec54fa" + ] + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T14:26:24.426228557" + }, + "homo_sapiens - [gvcf_gz, tbi, bed, []], fasta, fai, dict, [], []": { + "content": [ + [ + [ + { + "id": "test" + }, + "1ab95fbc5ec55b208f3001572bec54fa" + ] + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T14:27:04.179308513" + }, + "homo_sapiens - [gvcf_gz, tbi, [], []], fasta, fai, dict, dbsnp, dbsnp_tbi": { + "content": [ + [ + [ + { + "id": "test" + }, + "9b7d476515e07e5486633c42abd86cc" + ] + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T14:26:43.9088684" + }, + "homo_sapiens - [gvcf, idx, [], []], fasta, fai, dict, [], [] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + ], + "tbi": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T14:19:57.615552867" + }, + "homo_sapiens - [gendb, bed, [], []], fasta, fai, dict, [], []": { + "content": [ + [ + [ + { + "id": "test" + }, + "1ab95fbc5ec55b208f3001572bec54fa" + ] + ], + [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,3c16cbf71737813609ad10d901d92ab3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T14:27:46.189794941" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 455aedbf..cfb2e190 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -12,8 +12,8 @@ process GATK4_HAPLOTYPECALLER { tuple val(meta2), path(fasta) tuple val(meta3), path(fai) tuple val(meta4), path(dict) - path(dbsnp) - path(dbsnp_tbi) + tuple val(meta5), path(dbsnp) + tuple val(meta6), path(dbsnp_tbi) output: tuple val(meta), path("*.vcf.gz") , emit: vcf diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test index a124bff5..18d35f49 100644 --- a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test +++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test @@ -17,14 +17,14 @@ nextflow_process { """ input[0] = [ [ id:'test_bam' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [], [] ] - input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ] + input[1] = [ [ id:'test_fa' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'test_dict' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] input[4] = [ [], [] ] input[5] = [ [], [] ] @@ -35,9 +35,12 @@ nextflow_process { then { assertAll( { assert process.success }, - // { assert snapshot(process.out).match() }, // Unstable hashes - { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_bam_input") }, - { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_bam_input") }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.versions + ).match() + } ) } @@ -50,14 +53,14 @@ nextflow_process { """ input[0] = [ [ id:'test_cram' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [], [] ] - input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ] + input[1] = [ [ id:'test_fa' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'test_dict' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] input[4] = [ [], [] ] input[5] = [ [], [] ] """ @@ -67,9 +70,12 @@ nextflow_process { then { assertAll( { assert process.success }, - // { assert snapshot(process.out).match() }, // Unstable hashes - { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_input") }, - { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_input") }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.versions + ).match() + } ) } @@ -82,16 +88,16 @@ nextflow_process { """ input[0] = [ [ id:'test_cram_sites' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [], [] ] - input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ] - input[4] = [ [ id:'test_sites' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ] - input[5] = [ [ id:'test_sites_tbi' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) ] + input[1] = [ [ id:'test_fa' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'test_dict' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] + input[4] = [ [ id:'test_sites' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true) ] + input[5] = [ [ id:'test_sites_tbi' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true) ] """ } } @@ -99,9 +105,12 @@ nextflow_process { then { assertAll( { assert process.success }, - // { assert snapshot(process.out).match() }, // Unstable hashes - { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_input_with_sites") }, - { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_input_with_sites") }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.versions + ).match() + } ) } @@ -114,16 +123,16 @@ nextflow_process { """ input[0] = [ [ id:'test_cram_sites_dragstr' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_dragstrmodel'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt', checkIfExists: true) ] - input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ] - input[4] = [ [ id:'test_sites' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ] - input[5] = [ [ id:'test_sites_tbi' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) ] + input[1] = [ [ id:'test_fa' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'test_dict' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] + input[4] = [ [ id:'test_sites' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true) ] + input[5] = [ [ id:'test_sites_tbi' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true) ] """ } } @@ -131,9 +140,12 @@ nextflow_process { then { assertAll( { assert process.success }, - // { assert snapshot(process.out).match() }, // Unstable hashes - { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_dragstr_input_with_sites") }, - { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_dragstr_input_with_sites") }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.versions + ).match() + } ) } diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap index 375025ee..0203fcfc 100644 --- a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap @@ -1,82 +1,58 @@ { - "gatk_hc_vcf_cram_dragstr_input_with_sites": { + "homo_sapiens - [cram, crai] - fasta - fai - dict": { "content": [ - "test_cram_sites_dragstr.vcf.gz" + "test_cram.vcf.gz", + "test_cram.vcf.gz.tbi", + [ + "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-20T13:24:45.142682" + "timestamp": "2024-08-14T09:36:54.158605" }, - "gatk_hc_vcf_bam_input": { + "homo_sapiens - [cram, crai] - fasta - fai - dict - sites - sites_tbi": { "content": [ - "test_bam.vcf.gz" + "test_cram_sites.vcf.gz", + "test_cram_sites.vcf.gz.tbi", + [ + "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-20T13:23:19.203837" + "timestamp": "2024-08-14T09:37:13.77024" }, - "gatk_hc_vcf_cram_input": { + "homo_sapiens - [bam, bai] - fasta - fai - dict": { "content": [ - "test_cram.vcf.gz" + "test_bam.vcf.gz", + "test_bam.vcf.gz.tbi", + [ + "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-20T13:23:48.434615" + "timestamp": "2024-08-14T09:36:34.77631" }, - "gatk_hc_vcf_cram_input_with_sites": { + "homo_sapiens - [cram, crai, dragstr_model] - fasta - fai - dict - sites - sites_tbi": { "content": [ - "test_cram_sites.vcf.gz" + "test_cram_sites_dragstr.vcf.gz", + "test_cram_sites_dragstr.vcf.gz.tbi", + [ + "versions.yml:md5,05431a0ab28c85412c8b3582e863a7ab" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-02-20T13:24:17.147745" - }, - "gatk_hc_vcf_tbi_bam_input": { - "content": [ - "test_bam.vcf.gz.tbi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-20T13:23:19.23048" - }, - "gatk_hc_vcf_tbi_cram_input": { - "content": [ - "test_cram.vcf.gz.tbi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-20T13:23:48.45958" - }, - "gatk_hc_vcf_tbi_cram_dragstr_input_with_sites": { - "content": [ - "test_cram_sites_dragstr.vcf.gz.tbi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-20T13:24:45.154818" - }, - "gatk_hc_vcf_tbi_cram_input_with_sites": { - "content": [ - "test_cram_sites.vcf.gz.tbi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-20T13:24:17.158138" + "timestamp": "2024-08-14T09:37:32.967085" } } \ No newline at end of file diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml index 34513c7f..3d98a08b 100644 --- a/modules/nf-core/gawk/environment.yml +++ b/modules/nf-core/gawk/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - anaconda::gawk=5.1.0 + - conda-forge::gawk=5.3.0 diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf index f856a1f8..ca468929 100644 --- a/modules/nf-core/gawk/main.nf +++ b/modules/nf-core/gawk/main.nf @@ -4,8 +4,8 @@ process GAWK { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gawk:5.1.0' : - 'biocontainers/gawk:5.1.0' }" + 'https://depot.galaxyproject.org/singularity/gawk:5.3.0' : + 'biocontainers/gawk:5.3.0' }" input: tuple val(meta), path(input) @@ -41,10 +41,11 @@ process GAWK { stub: prefix = task.ext.prefix ?: "${meta.id}" - suffix = task.ext.suffix ?: "${input.getExtension}" + suffix = task.ext.suffix ?: "${input.getExtension()}" + def create_cmd = suffix.endsWith("gz") ? "echo '' | gzip >" : "touch" """ - touch ${prefix}.${suffix} + ${create_cmd} ${prefix}.${suffix} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/gawk/tests/main.nf.test b/modules/nf-core/gawk/tests/main.nf.test new file mode 100644 index 00000000..fce82ca9 --- /dev/null +++ b/modules/nf-core/gawk/tests/main.nf.test @@ -0,0 +1,56 @@ +nextflow_process { + + name "Test Process GAWK" + script "../main.nf" + process "GAWK" + + tag "modules" + tag "modules_nfcore" + tag "gawk" + + test("convert fasta to bed") { + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("convert fasta to bed with program file") { + config "./nextflow_with_program_file.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = Channel.of('BEGIN {FS="\t"}; {print \$1 FS "0" FS \$2}').collectFile(name:"program.txt") + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/gawk/tests/main.nf.test.snap b/modules/nf-core/gawk/tests/main.nf.test.snap new file mode 100644 index 00000000..4f3a759c --- /dev/null +++ b/modules/nf-core/gawk/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "convert fasta to bed with program file": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-05-17T15:20:02.495430346" + }, + "convert fasta to bed": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-05-17T15:19:53.291809648" + } +} \ No newline at end of file diff --git a/modules/nf-core/gawk/tests/nextflow.config b/modules/nf-core/gawk/tests/nextflow.config new file mode 100644 index 00000000..6e5d43a3 --- /dev/null +++ b/modules/nf-core/gawk/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + withName: GAWK { + ext.suffix = "bed" + ext.args2 = '\'BEGIN {FS="\t"}; {print \$1 FS "0" FS \$2}\'' + } +} diff --git a/modules/nf-core/gawk/tests/nextflow_with_program_file.config b/modules/nf-core/gawk/tests/nextflow_with_program_file.config new file mode 100644 index 00000000..693ad419 --- /dev/null +++ b/modules/nf-core/gawk/tests/nextflow_with_program_file.config @@ -0,0 +1,5 @@ +process { + withName: GAWK { + ext.suffix = "bed" + } +} diff --git a/modules/nf-core/gawk/tests/tags.yml b/modules/nf-core/gawk/tests/tags.yml new file mode 100644 index 00000000..72e4531d --- /dev/null +++ b/modules/nf-core/gawk/tests/tags.yml @@ -0,0 +1,2 @@ +gawk: + - "modules/nf-core/gawk/**" diff --git a/modules/nf-core/happy/happy/environment.yml b/modules/nf-core/happy/happy/environment.yml deleted file mode 100644 index 3d29dcb2..00000000 --- a/modules/nf-core/happy/happy/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: happy_happy -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::hap.py=0.3.14 diff --git a/modules/nf-core/happy/happy/main.nf b/modules/nf-core/happy/happy/main.nf deleted file mode 100644 index b3cc12d5..00000000 --- a/modules/nf-core/happy/happy/main.nf +++ /dev/null @@ -1,84 +0,0 @@ -process HAPPY_HAPPY { - tag "$meta.id" - label 'process_medium' - - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0': - 'biocontainers/hap.py:0.3.14--py27h5c5a3ab_0' }" - - input: - tuple val(meta), path(query_vcf), path(truth_vcf), path(regions_bed), path(targets_bed) - tuple val(meta2), path(fasta) - tuple val(meta3), path(fasta_fai) - tuple val(meta4), path(false_positives_bed) - tuple val(meta5), path(stratification_tsv) - tuple val(meta6), path(stratification_beds) - - output: - tuple val(meta), path('*.summary.csv') , emit: summary_csv - tuple val(meta), path('*.roc.all.csv.gz') , emit: roc_all_csv - tuple val(meta), path('*.roc.Locations.INDEL.csv.gz') , emit: roc_indel_locations_csv - tuple val(meta), path('*.roc.Locations.INDEL.PASS.csv.gz') , emit: roc_indel_locations_pass_csv - tuple val(meta), path('*.roc.Locations.SNP.csv.gz') , emit: roc_snp_locations_csv - tuple val(meta), path('*.roc.Locations.SNP.PASS.csv.gz') , emit: roc_snp_locations_pass_csv - tuple val(meta), path('*.extended.csv') , emit: extended_csv - tuple val(meta), path('*.runinfo.json') , emit: runinfo - tuple val(meta), path('*.metrics.json.gz') , emit: metrics_json - tuple val(meta), path('*.vcf.gz') , emit: vcf, optional:true - tuple val(meta), path('*.tbi') , emit: tbi, optional:true - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def regions = regions_bed ? "-R ${regions_bed}" : "" - def targets = targets_bed ? "-T ${targets_bed}" : "" - def false_positives = false_positives_bed ? "--false-positives ${false_positives_bed}" : "" - def stratification = stratification_tsv ? "--stratification ${stratification_tsv}" : "" - def VERSION = '0.3.14' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - """ - hap.py \\ - ${truth_vcf} \\ - ${query_vcf} \\ - ${args} \\ - --reference ${fasta} \\ - --threads ${task.cpus} \\ - ${regions} \\ - ${targets} \\ - ${false_positives} \\ - ${stratification} \\ - -o ${prefix} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hap.py: $VERSION - END_VERSIONS - """ - - stub: - def args = task.ext.args ?: '' - def VERSION = '0.3.14' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - """ - touch ${prefix}.summary.csv - touch ${prefix}.roc.all.csv.gz - touch ${prefix}.roc.Locations.INDEL.csv.gz - touch ${prefix}.roc.Locations.INDEL.PASS.csv.gz - touch ${prefix}.roc.Locations.SNP.csv.gz - touch ${prefix}.roc.Locations.SNP.PASS.csv.gz - touch ${prefix}.extended.csv - touch ${prefix}.runinfo.json - touch ${prefix}.metrics.json.gz - touch ${prefix}.vcf.gz - touch ${prefix}.vcf.gz.tbi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hap.py: $VERSION - END_VERSIONS - """ -} diff --git a/modules/nf-core/happy/happy/meta.yml b/modules/nf-core/happy/happy/meta.yml deleted file mode 100644 index 85912cb5..00000000 --- a/modules/nf-core/happy/happy/meta.yml +++ /dev/null @@ -1,114 +0,0 @@ -name: "happy_happy" -description: Hap.py is a tool to compare diploid genotypes at haplotype level. Rather than comparing VCF records row by row, hap.py will generate and match alternate sequences in a superlocus. A superlocus is a small region of the genome (sized between 1 and around 1000 bp) that contains one or more variants. -keywords: - - happy - - benchmark - - haplotype - - validation -tools: - - "happy": - description: "Haplotype VCF comparison tools" - homepage: "https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/hap-py-benchmarking.html" - documentation: "https://github.com/Illumina/hap.py" - tool_dev_url: "https://github.com/Illumina/hap.py" - licence: "['BSD-2-clause']" -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - query_vcf: - type: file - description: VCF/GVCF file to query - pattern: "*.{gvcf,vcf}.gz" - - truth_vcf: - type: file - description: gold standard VCF file - pattern: "*.{gvcf,vcf}.gz" - - regions_bed: - type: file - description: Sparse regions to restrict the analysis to - pattern: "*.bed" - - targets_bed: - type: file - description: Dense regions to restrict the analysis to - pattern: "*.bed" - - fasta: - type: file - description: FASTA file of the reference genome - pattern: "*.{fa,fasta}" - - fasta_fai: - type: file - description: The index of the reference FASTA - pattern: "*.fai" - - false_positives_bed: - type: file - description: False positive / confident call regions. Calls outside these regions will be labelled as UNK. - pattern: "*.{bed,bed.gz}" - - stratification_tsv: - type: file - description: Stratification file list in TSV format - pattern: "*.tsv" - - stratification_beds: - type: file(s) - description: One or more BED files used for stratification (these should be referenced in the stratification TSV) - pattern: "*.bed" -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - summary_csv: - type: file - description: A CSV file containing the summary of the benchmarking - pattern: "*.summary.csv" - - roc_all_csv: - type: file - description: A CSV file containing ROC values for all variants - pattern: "*.roc.all.csv.gz" - - roc_indel_locations_csv: - type: file - description: A CSV file containing ROC values for all indels - pattern: "*.roc.Locations.INDEL.csv.gz" - - roc_indel_locations_pass_csv: - type: file - description: A CSV file containing ROC values for all indels that passed all filters - pattern: "*.roc.Locations.INDEL.PASS.csv.gz" - - roc_snp_locations_csv: - type: file - description: A CSV file containing ROC values for all SNPs - pattern: "*.roc.Locations.SNP.csv.gz" - - roc_snp_locations_pass_csv: - type: file - description: A CSV file containing ROC values for all SNPs that passed all filters - pattern: "*.roc.Locations.SNP.PASS.csv.gz" - - extended_csv: - type: file - description: A CSV file containing extended info of the benchmarking - pattern: "*.extended.csv" - - json: - type: file - description: A JSON file containing the run info - pattern: "*.runinfo.json" - - runinfo: - type: file - description: A JSON file containing the benchmarking metrics - pattern: "*.metrics.json.gz" - - vcf: - type: file - description: An annotated VCF - pattern: "*.vcf.gz" - - tbi: - type: file - description: The index of the annotated VCF - pattern: "*.tbi" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@nvnieuwk" -maintainers: - - "@nvnieuwk" diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml index 88c7126c..bcb9d64a 100644 --- a/modules/nf-core/mosdepth/environment.yml +++ b/modules/nf-core/mosdepth/environment.yml @@ -5,4 +5,4 @@ channels: - defaults dependencies: # renovate: datasource=conda depName=bioconda/mosdepth - - mosdepth=0.3.6 + - mosdepth=0.3.8 diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index c7e24303..6f4a8383 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -4,8 +4,8 @@ process MOSDEPTH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.6--hd299d5a_0' : - 'biocontainers/mosdepth:0.3.6--hd299d5a_0'}" + 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.8--hd299d5a_0' : + 'biocontainers/mosdepth:0.3.8--hd299d5a_0'}" input: tuple val(meta), path(bam), path(bai), path(bed) @@ -63,13 +63,13 @@ process MOSDEPTH { touch ${prefix}.region.dist.txt touch ${prefix}.summary.txt touch ${prefix}.per-base.d4 - touch ${prefix}.per-base.bed.gz + echo "" | gzip > ${prefix}.per-base.bed.gz touch ${prefix}.per-base.bed.gz.csi - touch ${prefix}.regions.bed.gz + echo "" | gzip > ${prefix}.regions.bed.gz touch ${prefix}.regions.bed.gz.csi - touch ${prefix}.quantized.bed.gz + echo "" | gzip > ${prefix}.quantized.bed.gz touch ${prefix}.quantized.bed.gz.csi - touch ${prefix}.thresholds.bed.gz + echo "" | gzip > ${prefix}.thresholds.bed.gz touch ${prefix}.thresholds.bed.gz.csi cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/mosdepth/tests/main.nf.test b/modules/nf-core/mosdepth/tests/main.nf.test index d991f819..0b3c860d 100644 --- a/modules/nf-core/mosdepth/tests/main.nf.test +++ b/modules/nf-core/mosdepth/tests/main.nf.test @@ -15,8 +15,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] ] input[1] = [[],[]] @@ -40,9 +40,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [[],[]] """ @@ -65,13 +65,13 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [] ] input[1] = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] """ } @@ -93,13 +93,13 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] """ } @@ -122,8 +122,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] ] input[1] = [[],[]] @@ -148,8 +148,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] ] input[1] = [[],[]] @@ -174,9 +174,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [[],[]] """ @@ -200,9 +200,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [[],[]] """ @@ -225,9 +225,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [[],[]] """ @@ -237,21 +237,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.global_txt[0][1]).name, - file(process.out.summary_txt[0][1]).name, - file(process.out.regions_txt[0][1]).name, - file(process.out.per_base_d4[0][1]).name, - file(process.out.per_base_bed[0][1]).name, - file(process.out.per_base_csi[0][1]).name, - file(process.out.regions_bed[0][1]).name, - file(process.out.regions_csi[0][1]).name, - file(process.out.quantized_bed[0][1]).name, - file(process.out.quantized_csi[0][1]).name, - file(process.out.thresholds_bed[0][1]).name, - file(process.out.thresholds_csi[0][1]).name, - process.out.versions - ).match() } + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/mosdepth/tests/main.nf.test.snap b/modules/nf-core/mosdepth/tests/main.nf.test.snap index dc4d9508..c604540b 100644 --- a/modules/nf-core/mosdepth/tests/main.nf.test.snap +++ b/modules/nf-core/mosdepth/tests/main.nf.test.snap @@ -1,23 +1,236 @@ { "homo_sapiens - bam, bai, [] - stub": { "content": [ - "test.global.dist.txt", - "test.summary.txt", - "test.region.dist.txt", - "test.per-base.d4", - "test.per-base.bed.gz", - "test.per-base.bed.gz.csi", - "test.regions.bed.gz", - "test.regions.bed.gz.csi", - "test.quantized.bed.gz", - "test.quantized.bed.gz.csi", - "test.thresholds.bed.gz", - "test.thresholds.bed.gz.csi", - [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.global.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + [ + { + "id": "test", + "single_end": true + }, + "test.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "11": [ + [ + { + "id": "test", + "single_end": true + }, + "test.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "12": [ + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + ], + "2": [ + [ + { + "id": "test", + "single_end": true + }, + "test.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + [ + { + "id": "test", + "single_end": true + }, + "test.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "7": [ + [ + { + "id": "test", + "single_end": true + }, + "test.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + { + "id": "test", + "single_end": true + }, + "test.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "9": [ + [ + { + "id": "test", + "single_end": true + }, + "test.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "global_txt": [ + [ + { + "id": "test", + "single_end": true + }, + "test.global.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "per_base_bed": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "per_base_csi": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "per_base_d4": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "quantized_bed": [ + [ + { + "id": "test", + "single_end": true + }, + "test.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "quantized_csi": [ + [ + { + "id": "test", + "single_end": true + }, + "test.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "regions_bed": [ + [ + { + "id": "test", + "single_end": true + }, + "test.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "regions_csi": [ + [ + { + "id": "test", + "single_end": true + }, + "test.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "regions_txt": [ + [ + { + "id": "test", + "single_end": true + }, + "test.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "summary_txt": [ + [ + { + "id": "test", + "single_end": true + }, + "test.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "thresholds_bed": [ + [ + { + "id": "test", + "single_end": true + }, + "test.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "thresholds_csi": [ + [ + { + "id": "test", + "single_end": true + }, + "test.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + ] + } ], - "timestamp": "2023-11-27T15:14:34.897155161" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:33:16.953408231" }, "homo_sapiens - cram, crai, bed": { "content": [ @@ -47,7 +260,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -67,7 +280,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -76,7 +289,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -85,7 +298,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "7": [ @@ -94,7 +307,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "8": [ @@ -118,7 +331,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -127,7 +340,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -145,7 +358,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "regions_csi": [ @@ -154,7 +367,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "regions_txt": [ @@ -182,11 +395,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:47:18.171150781" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:32:50.160217828" }, "homo_sapiens - bam, bai, [] - quantized": { "content": [ @@ -216,7 +433,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ @@ -230,7 +447,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -239,7 +456,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -254,7 +471,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz:md5,3e434a8bafcf59a67841ae3d4d752838" + "test.quantized.bed.gz:md5,f037c215449d361112efc10108fcc17c" ] ], "9": [ @@ -263,7 +480,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93" + "test.quantized.bed.gz.csi:md5,4f69e6ace50206a2768be66ded3a56f0" ] ], "global_txt": [ @@ -281,7 +498,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -290,7 +507,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -302,7 +519,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz:md5,3e434a8bafcf59a67841ae3d4d752838" + "test.quantized.bed.gz:md5,f037c215449d361112efc10108fcc17c" ] ], "quantized_csi": [ @@ -311,7 +528,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93" + "test.quantized.bed.gz.csi:md5,4f69e6ace50206a2768be66ded3a56f0" ] ], "regions_bed": [ @@ -339,11 +556,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:47:29.228103864" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:33:01.164885111" }, "homo_sapiens - bam, bai, bed": { "content": [ @@ -373,7 +594,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -393,7 +614,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -402,7 +623,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -411,7 +632,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "7": [ @@ -420,7 +641,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "8": [ @@ -444,7 +665,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -453,7 +674,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -471,7 +692,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "regions_csi": [ @@ -480,7 +701,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "regions_txt": [ @@ -508,11 +729,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:47:04.537716314" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:32:39.071657456" }, "homo_sapiens - bam, bai, [] - window": { "content": [ @@ -542,7 +767,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -550,7 +775,7 @@ "id": "test", "single_end": true }, - "test.mosdepth.region.dist.txt:md5,39e0e707ec32feb5176fd20a95f1f468" + "test.mosdepth.region.dist.txt:md5,0b6ea9f0da1228252d9aef2d3b6f7f76" ] ], "3": [ @@ -562,7 +787,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -571,7 +796,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -580,7 +805,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,f02e2cb49cc050e13d76942d6960827a" + "test.regions.bed.gz:md5,34f48d16fcdd61e44d812e29e02c77b8" ] ], "7": [ @@ -589,7 +814,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d" + "test.regions.bed.gz.csi:md5,2a30bcb7f5c7632136b3efce24723970" ] ], "8": [ @@ -613,7 +838,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -622,7 +847,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -640,7 +865,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,f02e2cb49cc050e13d76942d6960827a" + "test.regions.bed.gz:md5,34f48d16fcdd61e44d812e29e02c77b8" ] ], "regions_csi": [ @@ -649,7 +874,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d" + "test.regions.bed.gz.csi:md5,2a30bcb7f5c7632136b3efce24723970" ] ], "regions_txt": [ @@ -658,7 +883,7 @@ "id": "test", "single_end": true }, - "test.mosdepth.region.dist.txt:md5,39e0e707ec32feb5176fd20a95f1f468" + "test.mosdepth.region.dist.txt:md5,0b6ea9f0da1228252d9aef2d3b6f7f76" ] ], "summary_txt": [ @@ -677,11 +902,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:47:23.708536171" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:32:55.631776118" }, "homo_sapiens - bam, bai, []": { "content": [ @@ -711,7 +940,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ @@ -725,7 +954,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -734,7 +963,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -764,7 +993,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -773,7 +1002,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -810,11 +1039,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:46:56.975710077" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:32:33.642125299" }, "homo_sapiens - cram, crai, []": { "content": [ @@ -844,7 +1077,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ @@ -858,7 +1091,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -867,7 +1100,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -897,7 +1130,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -906,7 +1139,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -943,11 +1176,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:47:12.09259995" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:32:44.704920941" }, "homo_sapiens - bam, bai, bed - thresholds": { "content": [ @@ -976,7 +1213,7 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz:md5,13101e326eea3cbfa1d569b69f494f4c" + "test.thresholds.bed.gz:md5,fe70ae728cd10726c42a2bcd44adfc9d" ] ], "11": [ @@ -985,11 +1222,11 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196" + "test.thresholds.bed.gz.csi:md5,219414a0751185adb98d2235d83ea055" ] ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -1009,7 +1246,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -1018,7 +1255,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -1027,7 +1264,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "7": [ @@ -1036,7 +1273,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "8": [ @@ -1060,7 +1297,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -1069,7 +1306,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -1087,7 +1324,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "regions_csi": [ @@ -1096,7 +1333,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "regions_txt": [ @@ -1123,7 +1360,7 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz:md5,13101e326eea3cbfa1d569b69f494f4c" + "test.thresholds.bed.gz:md5,fe70ae728cd10726c42a2bcd44adfc9d" ] ], "thresholds_csi": [ @@ -1132,14 +1369,18 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196" + "test.thresholds.bed.gz.csi:md5,219414a0751185adb98d2235d83ea055" ] ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:49:44.311847326" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:33:06.737266831" } } \ No newline at end of file diff --git a/modules/nf-core/rtgtools/pedfilter/main.nf b/modules/nf-core/rtgtools/pedfilter/main.nf index bb36cf50..c06a33fa 100644 --- a/modules/nf-core/rtgtools/pedfilter/main.nf +++ b/modules/nf-core/rtgtools/pedfilter/main.nf @@ -11,8 +11,8 @@ process RTGTOOLS_PEDFILTER { tuple val(meta), path(input) output: - tuple val(meta), path("*.vcf.gz") , emit: output - path "versions.yml" , emit: versions + tuple val(meta), path("*.{vcf.gz,ped}") , emit: output + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -31,12 +31,11 @@ process RTGTOOLS_PEDFILTER { def postprocess = extension == "vcf.gz" ? "| rtg bgzip ${args2} -" : "" """ - cut -f1-6 ${input} > ${prefix}.ped - rtg pedfilter \\ ${args} \\ - ${prefix}.ped \\ - | head -n -1 ${postprocess} > ${prefix}.${extension} + ${input} \\ + | head -n -1 \\ + ${postprocess} > ${prefix}.${extension} cat <<-END_VERSIONS > versions.yml @@ -46,7 +45,6 @@ process RTGTOOLS_PEDFILTER { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def extension = args.contains("--vcf") ? "vcf.gz" : "ped" diff --git a/modules/nf-core/rtgtools/pedfilter/meta.yml b/modules/nf-core/rtgtools/pedfilter/meta.yml index 785ac990..4e90fd7b 100644 --- a/modules/nf-core/rtgtools/pedfilter/meta.yml +++ b/modules/nf-core/rtgtools/pedfilter/meta.yml @@ -11,7 +11,7 @@ tools: homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" - licence: "['BSD']" + licence: ["BSD"] input: - meta: type: map diff --git a/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff b/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff index 4463e941..18590bf8 100644 --- a/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff +++ b/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff @@ -1,39 +1,19 @@ Changes in module 'nf-core/rtgtools/pedfilter' +Changes in 'rtgtools/pedfilter/main.nf': --- modules/nf-core/rtgtools/pedfilter/main.nf +++ modules/nf-core/rtgtools/pedfilter/main.nf -@@ -11,8 +11,8 @@ - tuple val(meta), path(input) - - output: -- tuple val(meta), path("*.{vcf.gz,ped}") , emit: output -- path "versions.yml" , emit: versions -+ tuple val(meta), path("*.vcf.gz") , emit: output -+ path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when -@@ -31,10 +31,12 @@ - def postprocess = extension == "vcf.gz" ? "| rtg bgzip ${args2} -" : "" - - """ -+ cut -f1-6 ${input} > ${prefix}.ped -+ +@@ -34,6 +34,7 @@ rtg pedfilter \\ ${args} \\ -- ${input} \\ -- ${postprocess} > ${prefix}.${extension} -+ ${prefix}.ped \\ -+ | head -n -1 ${postprocess} > ${prefix}.${extension} - - - cat <<-END_VERSIONS > versions.yml -@@ -44,6 +46,7 @@ - """ + ${input} \\ ++ | head -n -1 \\ + ${postprocess} > ${prefix}.${extension} - stub: -+ def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def extension = args.contains("--vcf") ? "vcf.gz" : "ped" +'modules/nf-core/rtgtools/pedfilter/environment.yml' is unchanged +'modules/nf-core/rtgtools/pedfilter/meta.yml' is unchanged +'modules/nf-core/rtgtools/pedfilter/tests/main.nf.test' is unchanged +'modules/nf-core/rtgtools/pedfilter/tests/main.nf.test.snap' is unchanged +'modules/nf-core/rtgtools/pedfilter/tests/nextflow.config' is unchanged ************************************************************ diff --git a/modules/nf-core/rtgtools/pedfilter/tests/main.nf.test b/modules/nf-core/rtgtools/pedfilter/tests/main.nf.test new file mode 100644 index 00000000..0ddcebdb --- /dev/null +++ b/modules/nf-core/rtgtools/pedfilter/tests/main.nf.test @@ -0,0 +1,85 @@ + +nextflow_process { + + name "Test Process RTGTOOLS_PEDFILTER" + script "../main.nf" + process "RTGTOOLS_PEDFILTER" + + tag "modules" + tag "modules_nfcore" + tag "rtgtools" + tag "rtgtools/pedfilter" + + test("test-rtgtools-pedfilter-ped") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-rtgtools-pedfilter-vcf") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-rtgtools-pedfilter-vcf-output") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.output[0][1]).linesGzip[3..7], + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/rtgtools/pedfilter/tests/main.nf.test.snap b/modules/nf-core/rtgtools/pedfilter/tests/main.nf.test.snap new file mode 100644 index 00000000..7475fa8b --- /dev/null +++ b/modules/nf-core/rtgtools/pedfilter/tests/main.nf.test.snap @@ -0,0 +1,91 @@ +{ + "test-rtgtools-pedfilter-vcf": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped:md5,342135c8bf22e573367b75ef5e1c5e6b" + ] + ], + "1": [ + "versions.yml:md5,036d97d5be26fce2e7d956034b9dc86d" + ], + "output": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped:md5,342135c8bf22e573367b75ef5e1c5e6b" + ] + ], + "versions": [ + "versions.yml:md5,036d97d5be26fce2e7d956034b9dc86d" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T16:11:01.797205" + }, + "test-rtgtools-pedfilter-vcf-output": { + "content": [ + [ + "##CL=pedfilter --vcf justhusky.ped", + "##diseased=hugelymodelbat", + "##SAMPLE=", + "##SAMPLE=", + "##SAMPLE=" + ], + [ + "versions.yml:md5,036d97d5be26fce2e7d956034b9dc86d" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T20:46:00.069224" + }, + "test-rtgtools-pedfilter-ped": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped:md5,a8b8f6538e1738d6e06fddfe15d36f09" + ] + ], + "1": [ + "versions.yml:md5,036d97d5be26fce2e7d956034b9dc86d" + ], + "output": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ped:md5,a8b8f6538e1738d6e06fddfe15d36f09" + ] + ], + "versions": [ + "versions.yml:md5,036d97d5be26fce2e7d956034b9dc86d" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T16:10:53.473351" + } +} \ No newline at end of file diff --git a/modules/nf-core/rtgtools/pedfilter/tests/nextflow.config b/modules/nf-core/rtgtools/pedfilter/tests/nextflow.config new file mode 100644 index 00000000..a8a3ec54 --- /dev/null +++ b/modules/nf-core/rtgtools/pedfilter/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'RTGTOOLS_PEDFILTER' { + ext.args = "--vcf" + } +} diff --git a/modules/nf-core/rtgtools/rocplot/meta.yml b/modules/nf-core/rtgtools/rocplot/meta.yml index 927cff90..2b4d43d7 100644 --- a/modules/nf-core/rtgtools/rocplot/meta.yml +++ b/modules/nf-core/rtgtools/rocplot/meta.yml @@ -11,7 +11,7 @@ tools: homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" - licence: "['BSD']" + licence: ["BSD"] input: - meta: type: map diff --git a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test index 160eafcf..c7c37084 100644 --- a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test +++ b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test @@ -7,6 +7,8 @@ nextflow_process { tag "modules_nfcore" tag "rtgtools" tag "rtgtools/rocplot" + tag "rtgtools/vcfeval" + tag "untar" test("homo_sapiens - tsv") { @@ -17,7 +19,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_21_sdf']) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome_sdf.tar.gz', checkIfExists: true) ] """ } @@ -29,12 +31,12 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = UNTAR.out.untar println(projectDir) diff --git a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test.snap b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test.snap index 389ffb5b..f4dee3a1 100644 --- a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test.snap +++ b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test.snap @@ -5,6 +5,10 @@ "test.svg", "versions.yml" ], - "timestamp": "2023-10-24T12:48:36.35343056" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-09T10:44:42.642303" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml index cd4ee8c3..7a95ca61 100644 --- a/modules/nf-core/samtools/convert/environment.yml +++ b/modules/nf-core/samtools/convert/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index e2d679f7..03b7b525 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_CONVERT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(input), path(index) @@ -13,8 +13,11 @@ process SAMTOOLS_CONVERT { tuple val(meta3), path(fai) output: - tuple val(meta), path("*.{cram,bam}"), path("*.{crai,bai}") , emit: alignment_index - path "versions.yml" , emit: versions + tuple val(meta), path("*.bam") , emit: bam , optional: true + tuple val(meta), path("*.cram") , emit: cram, optional: true + tuple val(meta), path("*.bai") , emit: bai , optional: true + tuple val(meta), path("*.crai") , emit: crai, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -39,4 +42,19 @@ process SAMTOOLS_CONVERT { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def output_extension = input.getExtension() == "bam" ? "cram" : "bam" + def index_extension = output_extension == "bam" ? "bai" : "crai" + + """ + touch ${prefix}.${output_extension} + touch ${prefix}.${index_extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/samtools/convert/meta.yml b/modules/nf-core/samtools/convert/meta.yml index f8a1612f..55828971 100644 --- a/modules/nf-core/samtools/convert/meta.yml +++ b/modules/nf-core/samtools/convert/meta.yml @@ -39,10 +39,22 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - alignment_index: + - bam: type: file - description: filtered/converted BAM/CRAM file + index - pattern: "*{.bam/cram,.bai/crai}" + description: filtered/converted BAM file + pattern: "*{.bam}" + - cram: + type: file + description: filtered/converted CRAM file + pattern: "*{cram}" + - bai: + type: file + description: filtered/converted BAM index + pattern: "*{.bai}" + - crai: + type: file + description: filtered/converted CRAM index + pattern: "*{.crai}" - version: type: file description: File containing software version @@ -53,3 +65,4 @@ authors: maintainers: - "@FriederikeHanssen" - "@maxulysse" + - "@matthdsm" diff --git a/modules/nf-core/samtools/convert/tests/main.nf.test b/modules/nf-core/samtools/convert/tests/main.nf.test index ee59532a..91a0c69e 100644 --- a/modules/nf-core/samtools/convert/tests/main.nf.test +++ b/modules/nf-core/samtools/convert/tests/main.nf.test @@ -34,9 +34,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.alignment_index[0][1]).name).match("bam_alignment_index_1") }, - { assert snapshot(file(process.out.alignment_index[0][2]).name).match("bam_alignment_index_2") }, - { assert snapshot(process.out.versions).match("bam_versions") } + { assert snapshot(file(process.out.cram[0][1]).name).match("bam_to_cram_alignment") }, + { assert snapshot(file(process.out.crai[0][1]).name).match("bam_to_cram_index") }, + { assert snapshot(process.out.versions).match("bam_to_cram_versions") } ) } } @@ -66,9 +66,41 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.alignment_index[0][1]).name).match("cram_alignment_index_1") }, - { assert snapshot(file(process.out.alignment_index[0][2]).name).match("cram_alignment_index_2") }, - { assert snapshot(process.out.versions).match("cram_versions") } + { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_alignment") }, + { assert snapshot(file(process.out.bai[0][1]).name).match("cram_to_bam_alignment_index") }, + { assert snapshot(process.out.versions).match("cram_to_bam_versions") } + ) + } + } + + test("sarscov2 - [bam, bai], fasta, fai - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'fai' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match("stub") } ) } } diff --git a/modules/nf-core/samtools/convert/tests/main.nf.test.snap b/modules/nf-core/samtools/convert/tests/main.nf.test.snap index 96ec9f4e..51362902 100644 --- a/modules/nf-core/samtools/convert/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/convert/tests/main.nf.test.snap @@ -1,66 +1,131 @@ { - "cram_alignment_index_1": { + "cram_to_bam_alignment": { "content": [ "test.bam" ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-02T17:04:16.431159" + "timestamp": "2024-03-06T11:14:51.300147176" }, - "cram_alignment_index_2": { + "bam_to_cram_alignment": { "content": [ - "test.bam.bai" + "test.cram" ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-02T17:04:16.43428" + "timestamp": "2024-03-06T11:14:36.625470184" }, - "bam_alignment_index_2": { + "cram_to_bam_versions": { "content": [ - "test.cram.crai" + [ + "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-02T17:00:29.669534" + "timestamp": "2024-05-28T15:44:34.618037105" }, - "bam_alignment_index_1": { + "bam_to_cram_versions": { "content": [ - "test.cram" + [ + "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-02T17:00:29.666821" + "timestamp": "2024-05-28T15:44:29.165839679" }, - "cram_versions": { + "stub": { "content": [ - [ - "versions.yml:md5,dd0aaf61f39c9ce91c74090f3c7ce1d0" - ] + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" + ], + "bai": [ + + ], + "bam": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" + ] + } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:14:38.224641326" + "timestamp": "2024-05-28T15:44:40.258233921" }, - "bam_versions": { + "bam_to_cram_index": { "content": [ - [ - "versions.yml:md5,dd0aaf61f39c9ce91c74090f3c7ce1d0" - ] + "test.cram.crai" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-06T11:14:36.640009334" + }, + "cram_to_bam_alignment_index": { + "content": [ + "test.bam.bai" ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:14:29.852388191" + "timestamp": "2024-03-06T11:14:51.304477426" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index 3e95dd71..f8450fa5 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -1,8 +1,10 @@ name: samtools_faidx + channels: - conda-forge - bioconda - defaults + dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index cfe7ad95..bdcdbc95 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FAIDX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index e189af28..f3c25de2 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -39,6 +39,10 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + - fa: + type: file + description: FASTA file + pattern: "*.{fa}" - fai: type: file description: FASTA index file diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test new file mode 100644 index 00000000..17244ef2 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test @@ -0,0 +1,122 @@ +nextflow_process { + + name "Test Process SAMTOOLS_FAIDX" + script "../main.nf" + process "SAMTOOLS_FAIDX" + + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/faidx" + + test("test_samtools_faidx") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_bgzip") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_fasta") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_stub_fasta") { + + config "./nextflow2.config" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_stub_fai") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap new file mode 100644 index 00000000..3223b72b --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -0,0 +1,249 @@ +{ + "test_samtools_faidx": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:14.779784761" + }, + "test_samtools_faidx_bgzip": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" + ] + ], + "3": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" + ] + ], + "versions": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:20.256633877" + }, + "test_samtools_faidx_fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ], + "fa": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36" + ] + ], + "fai": [ + + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:25.632577273" + }, + "test_samtools_faidx_stub_fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ], + "fa": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "fai": [ + + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:31.058424849" + }, + "test_samtools_faidx_stub_fai": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,2db78952923a61e05d50b95518b21856" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-28T15:42:36.479929617" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/tests/nextflow.config b/modules/nf-core/samtools/faidx/tests/nextflow.config new file mode 100644 index 00000000..f76a3ba0 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: SAMTOOLS_FAIDX { + ext.args = 'MT192765.1 -o extract.fa' + } + +} diff --git a/modules/nf-core/samtools/faidx/tests/nextflow2.config b/modules/nf-core/samtools/faidx/tests/nextflow2.config new file mode 100644 index 00000000..33ebbd5d --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/nextflow2.config @@ -0,0 +1,6 @@ +process { + + withName: SAMTOOLS_FAIDX { + ext.args = '-o extract.fa' + } +} diff --git a/modules/nf-core/samtools/faidx/tests/tags.yml b/modules/nf-core/samtools/faidx/tests/tags.yml new file mode 100644 index 00000000..e4a83948 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/faidx: + - modules/nf-core/samtools/faidx/** diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index a5e50649..260d516b 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index dc14f98d..e002585b 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(input) @@ -35,10 +35,11 @@ process SAMTOOLS_INDEX { """ stub: + def args = task.ext.args ?: '' + def extension = file(input).getExtension() == 'cram' ? + "crai" : args.contains("-c") ? "csi" : "bai" """ - touch ${input}.bai - touch ${input}.crai - touch ${input}.csi + touch ${input}.${extension} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test index bb7756d1..ca34fb5c 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -9,11 +9,7 @@ nextflow_process { tag "samtools/index" test("bai") { - when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -27,18 +23,13 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.bai).match("bai") }, - { assert snapshot(process.out.versions).match("bai_versions") } + { assert snapshot(process.out).match() } ) } } test("crai") { - when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -52,20 +43,83 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.crai).match("crai") }, - { assert snapshot(process.out.versions).match("crai_versions") } + { assert snapshot(process.out).match() } ) } } test("csi") { - config "./csi.nextflow.config" when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.csi[0][1]).name, + process.out.versions + ).match() } + ) + } + } + + test("bai - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("crai - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) + ]) + """ } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("csi - stub") { + options "-stub" + config "./csi.nextflow.config" + + when { process { """ input[0] = Channel.of([ @@ -79,8 +133,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert path(process.out.csi.get(0).get(1)).exists() }, - { assert snapshot(process.out.versions).match("csi_versions") } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 3dc8e7de..799d199c 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -1,74 +1,250 @@ { - "crai_versions": { + "csi - stub": { "content": [ - [ - "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" - ] + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + + ], + "crai": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-13T16:12:00.324667957" + "timestamp": "2024-07-22T16:51:53.9057" }, - "csi_versions": { + "crai - stub": { "content": [ - [ - "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" - ] + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-13T16:12:07.885103162" + "timestamp": "2024-07-22T16:51:45.931558" }, - "crai": { + "bai - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "crai": [ + + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-12T18:41:38.446424" + "timestamp": "2024-07-22T16:51:34.807525" }, - "bai": { + "csi": { "content": [ + "test.paired_end.sorted.bam.csi", [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" - ] + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-12T18:40:46.579747" + "timestamp": "2024-07-22T16:52:55.688799" }, - "bai_versions": { + "crai": { "content": [ - [ - "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" - ] + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T16:51:17.609533" + }, + "bai": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ], + "crai": [ + + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-13T16:11:51.641425452" + "timestamp": "2024-07-22T16:51:04.16585" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml index fc669b1b..cd366d6d 100644 --- a/modules/nf-core/samtools/merge/environment.yml +++ b/modules/nf-core/samtools/merge/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index a3048c28..693b1d80 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_MERGE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(input_files, stageAs: "?/*") diff --git a/modules/nf-core/samtools/merge/samtools-merge.diff b/modules/nf-core/samtools/merge/samtools-merge.diff deleted file mode 100644 index 59077e1f..00000000 --- a/modules/nf-core/samtools/merge/samtools-merge.diff +++ /dev/null @@ -1,13 +0,0 @@ -Changes in module 'nf-core/samtools/merge' ---- modules/nf-core/samtools/merge/main.nf -+++ modules/nf-core/samtools/merge/main.nf -@@ -1,6 +1,6 @@ - process SAMTOOLS_MERGE { - tag "$meta.id" -- label 'process_low' -+ label 'process_high' - - conda "bioconda::samtools=1.17" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - -************************************************************ diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test.snap b/modules/nf-core/samtools/merge/tests/main.nf.test.snap index f7da7699..17bc846f 100644 --- a/modules/nf-core/samtools/merge/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/merge/tests/main.nf.test.snap @@ -80,14 +80,14 @@ "bam_versions": { "content": [ [ - "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4" + "versions.yml:md5,84dab54b9812780df48f5cecef690c34" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:16:33.782637377" + "timestamp": "2024-05-28T15:46:35.851936597" }, "bams_csi": { "content": [ @@ -124,14 +124,14 @@ "bams_stub_versions": { "content": [ [ - "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4" + "versions.yml:md5,84dab54b9812780df48f5cecef690c34" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:16:42.594476052" + "timestamp": "2024-05-28T15:46:41.405707643" }, "bam_cram": { "content": [ @@ -158,14 +158,14 @@ "bams_versions": { "content": [ [ - "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4" + "versions.yml:md5,84dab54b9812780df48f5cecef690c34" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:16:04.805335656" + "timestamp": "2024-05-28T15:45:51.695689923" }, "crams_bam": { "content": [ @@ -182,14 +182,14 @@ "crams_versions": { "content": [ [ - "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4" + "versions.yml:md5,84dab54b9812780df48f5cecef690c34" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:16:25.889394689" + "timestamp": "2024-05-28T15:46:30.185392319" }, "bam_csi": { "content": [ diff --git a/modules/nf-core/snpeff/snpeff/main.nf b/modules/nf-core/snpeff/snpeff/main.nf index cc4f2ccb..28d13826 100644 --- a/modules/nf-core/snpeff/snpeff/main.nf +++ b/modules/nf-core/snpeff/snpeff/main.nf @@ -13,11 +13,11 @@ process SNPEFF_SNPEFF { tuple val(meta2), path(cache) output: - tuple val(meta), path("*.ann.vcf"), emit: vcf - path "*.csv" , emit: report - path "*.html" , emit: summary_html - path "*.genes.txt" , emit: genes_txt - path "versions.yml" , emit: versions + tuple val(meta), path("*.ann.vcf"), emit: vcf + tuple val(meta), path("*.csv"), emit: report + tuple val(meta), path("*.html"), emit: summary_html + tuple val(meta), path("*.genes.txt"), emit: genes_txt + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/snpeff/snpeff/tests/main.nf.test b/modules/nf-core/snpeff/snpeff/tests/main.nf.test new file mode 100644 index 00000000..803ff02c --- /dev/null +++ b/modules/nf-core/snpeff/snpeff/tests/main.nf.test @@ -0,0 +1,51 @@ +nextflow_process { + + name "Test Process SNPEFF_SNPEFF" + script "../main.nf" + process "SNPEFF_SNPEFF" + config "./nextflow.config" + tag "modules" + tag "modules_nfcore" + tag "modules_snpeff" + tag "snpeff" + tag "snpeff/download" + tag "snpeff/snpeff" + + test("test_SNPEFF_SNPEFF") { + + setup { + run("SNPEFF_DOWNLOAD") { + script "../../download/main.nf" + process { + """ + input[0] = Channel.of([[id:params.snpeff_genome + '.' + params.snpeff_cache_version], params.snpeff_genome, params.snpeff_cache_version]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ]) + input[1] = params.snpeff_genome + '.' + params.snpeff_cache_version + input[2] = SNPEFF_DOWNLOAD.out.cache + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.report[0][1]).exists() }, + { assert path(process.out.summary_html[0][1]).exists() }, + { assert path(process.out.vcf[0][1]).exists() }, + { assert snapshot(process.out.genes_txt).match("genes_txt") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } +} diff --git a/modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap b/modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap new file mode 100644 index 00000000..0891b844 --- /dev/null +++ b/modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap @@ -0,0 +1,31 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,25d44a118d558b331d51ec00be0d997c" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.02.0" + }, + "timestamp": "2024-03-18T17:37:18.879477" + }, + "genes_txt": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.genes.txt:md5,130536bf0237d7f3f746d32aaa32840a" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.02.0" + }, + "timestamp": "2024-03-18T17:37:18.874822" + } +} \ No newline at end of file diff --git a/modules/nf-core/snpeff/snpeff/tests/nextflow.config b/modules/nf-core/snpeff/snpeff/tests/nextflow.config new file mode 100644 index 00000000..d31ebf6b --- /dev/null +++ b/modules/nf-core/snpeff/snpeff/tests/nextflow.config @@ -0,0 +1,4 @@ +params { + snpeff_cache_version = "105" + snpeff_genome = "WBcel235" +} diff --git a/modules/nf-core/snpeff/snpeff/tests/tags.yml b/modules/nf-core/snpeff/snpeff/tests/tags.yml new file mode 100644 index 00000000..427b588d --- /dev/null +++ b/modules/nf-core/snpeff/snpeff/tests/tags.yml @@ -0,0 +1,2 @@ +snpeff/snpeff: + - "modules/nf-core/snpeff/snpeff/**" diff --git a/modules/nf-core/somalier/extract/environment.yml b/modules/nf-core/somalier/extract/environment.yml index e0dd11c9..72397774 100644 --- a/modules/nf-core/somalier/extract/environment.yml +++ b/modules/nf-core/somalier/extract/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::somalier=0.2.15 + - bioconda::somalier=0.2.19 diff --git a/modules/nf-core/somalier/extract/main.nf b/modules/nf-core/somalier/extract/main.nf index 8dc3c31c..703605d1 100644 --- a/modules/nf-core/somalier/extract/main.nf +++ b/modules/nf-core/somalier/extract/main.nf @@ -5,14 +5,14 @@ process SOMALIER_EXTRACT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/somalier:0.2.15--h37c5b7d_0': - 'biocontainers/somalier:0.2.15--h37c5b7d_0' }" + 'https://depot.galaxyproject.org/singularity/somalier:0.2.19--h0c29559_0': + 'biocontainers/somalier:0.2.19--h0c29559_0' }" input: tuple val(meta), path(input), path(input_index) - path(fasta) - path(fai) - path(sites) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(sites) output: tuple val(meta), path("*.somalier") , emit: extract diff --git a/modules/nf-core/somalier/extract/meta.yml b/modules/nf-core/somalier/extract/meta.yml index 7aa426ab..aabaf5d6 100644 --- a/modules/nf-core/somalier/extract/meta.yml +++ b/modules/nf-core/somalier/extract/meta.yml @@ -19,7 +19,7 @@ tools: documentation: "https://github.com/brentp/somalier/blob/master/README.md" tool_dev_url: "https://github.com/brentp/somalier" doi: "10.1186/s13073-020-00761-2" - licence: "MIT License" + licence: ["MIT"] input: - meta: type: map @@ -32,14 +32,29 @@ input: - input_index: type: file description: index file of the input data, e.g., bam.bai, cram.crai + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'hg38' ] - fasta: type: file description: The reference fasta file pattern: "*.{fasta,fna,fas,fa}" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'hg38' ] - fai: type: file description: FASTA index file pattern: "*.fai" + - meta4: + type: map + description: | + Groovy Map containing sites information + e.g. [ id:'hg38' ] - sites: type: file description: sites file in VCF format which can be taken from https://github.com/brentp/somalier diff --git a/modules/nf-core/somalier/extract/tests/main.nf.test b/modules/nf-core/somalier/extract/tests/main.nf.test new file mode 100644 index 00000000..dfc7e8a5 --- /dev/null +++ b/modules/nf-core/somalier/extract/tests/main.nf.test @@ -0,0 +1,84 @@ +nextflow_process { + + name "Test Process SOMALIER_EXTRACT" + script "../main.nf" + process "SOMALIER_EXTRACT" + + tag "modules" + tag "modules_nfcore" + tag "somalier" + tag "somalier/extract" + + test("homo_sapiens - [ bam, bai ], fasta, fai, sites") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'delete_me/somalier/sites_chr21.hg38.vcf.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - [ bam, bai ], fasta, fai, sites -stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'delete_me/somalier/sites_chr21.hg38.vcf.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/somalier/extract/tests/main.nf.test.snap b/modules/nf-core/somalier/extract/tests/main.nf.test.snap new file mode 100644 index 00000000..83df72a4 --- /dev/null +++ b/modules/nf-core/somalier/extract/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "homo_sapiens - [ bam, bai ], fasta, fai, sites": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "normal.somalier:md5,21f0b980edd42ddaa8ab964959c1de02" + ] + ], + "1": [ + "versions.yml:md5,df4e49e9520f49a862026da1aa81dde0" + ], + "extract": [ + [ + { + "id": "test", + "single_end": false + }, + "normal.somalier:md5,21f0b980edd42ddaa8ab964959c1de02" + ] + ], + "versions": [ + "versions.yml:md5,df4e49e9520f49a862026da1aa81dde0" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-01T13:25:23.384476049" + }, + "homo_sapiens - [ bam, bai ], fasta, fai, sites -stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.somalier:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,df4e49e9520f49a862026da1aa81dde0" + ], + "extract": [ + [ + { + "id": "test", + "single_end": false + }, + "test.somalier:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,df4e49e9520f49a862026da1aa81dde0" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-01T13:25:35.741711687" + } +} \ No newline at end of file diff --git a/modules/nf-core/somalier/extract/tests/tags.yml b/modules/nf-core/somalier/extract/tests/tags.yml new file mode 100644 index 00000000..836e3524 --- /dev/null +++ b/modules/nf-core/somalier/extract/tests/tags.yml @@ -0,0 +1,2 @@ +somalier/extract: + - "modules/nf-core/somalier/extract/**" diff --git a/modules/nf-core/somalier/relate/environment.yml b/modules/nf-core/somalier/relate/environment.yml index b8b70f67..5295646b 100644 --- a/modules/nf-core/somalier/relate/environment.yml +++ b/modules/nf-core/somalier/relate/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::somalier=0.2.15 + - bioconda::somalier=0.2.19 diff --git a/modules/nf-core/somalier/relate/main.nf b/modules/nf-core/somalier/relate/main.nf index a8188b64..1c0ba9ae 100644 --- a/modules/nf-core/somalier/relate/main.nf +++ b/modules/nf-core/somalier/relate/main.nf @@ -5,8 +5,8 @@ process SOMALIER_RELATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/somalier:0.2.15--h37c5b7d_0': - 'biocontainers/somalier:0.2.15--h37c5b7d_0' }" + 'https://depot.galaxyproject.org/singularity/somalier:0.2.19--h0c29559_0': + 'biocontainers/somalier:0.2.19--h0c29559_0' }" input: tuple val(meta), path(extract), path(ped) diff --git a/modules/nf-core/somalier/relate/meta.yml b/modules/nf-core/somalier/relate/meta.yml index d1d81c87..42638f4f 100644 --- a/modules/nf-core/somalier/relate/meta.yml +++ b/modules/nf-core/somalier/relate/meta.yml @@ -19,7 +19,7 @@ tools: documentation: "https://github.com/brentp/somalier/blob/master/README.md" tool_dev_url: "https://github.com/brentp/somalier" doi: "10.1186/s13073-020-00761-2" - licence: "MIT License" + licence: ["MIT"] input: - meta: type: map @@ -27,7 +27,7 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - extract: - type: file(s) + type: file description: extract file(s) from Somalier extract pattern: "*.somalier" - ped: diff --git a/modules/nf-core/somalier/relate/somalier-relate.diff b/modules/nf-core/somalier/relate/somalier-relate.diff index 48dc50f3..918d80b2 100644 --- a/modules/nf-core/somalier/relate/somalier-relate.diff +++ b/modules/nf-core/somalier/relate/somalier-relate.diff @@ -1,4 +1,5 @@ Changes in module 'nf-core/somalier/relate' +Changes in 'somalier/relate/main.nf': --- modules/nf-core/somalier/relate/main.nf +++ modules/nf-core/somalier/relate/main.nf @@ -16,6 +16,7 @@ @@ -27,4 +28,9 @@ Changes in module 'nf-core/somalier/relate' cat <<-END_VERSIONS > versions.yml "${task.process}": +'modules/nf-core/somalier/relate/environment.yml' is unchanged +'modules/nf-core/somalier/relate/meta.yml' is unchanged +'modules/nf-core/somalier/relate/tests/tags.yml' is unchanged +'modules/nf-core/somalier/relate/tests/main.nf.test' is unchanged +'modules/nf-core/somalier/relate/tests/main.nf.test.snap' is unchanged ************************************************************ diff --git a/modules/nf-core/somalier/relate/tests/main.nf.test b/modules/nf-core/somalier/relate/tests/main.nf.test new file mode 100644 index 00000000..5f17456d --- /dev/null +++ b/modules/nf-core/somalier/relate/tests/main.nf.test @@ -0,0 +1,124 @@ +nextflow_process { + + name "Test Process SOMALIER_RELATE" + script "../main.nf" + process "SOMALIER_RELATE" + + tag "modules" + tag "modules_nfcore" + tag "somalier" + tag "somalier/relate" + + test("[ delete_me, [] ], []") { + + when { + process { + """ + input[0] = [ + [ id:'cohort', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'delete_me/somalier/normal.somalier', checkIfExists: true), + file(params.modules_testdata_base_path + 'delete_me/somalier/tumour.somalier', checkIfExists: true) + ], + [] + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("[ delete_me, ped ], groups") { + + when { + process { + """ + input[0] = [ + [ id:'cohort', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'delete_me/somalier/normal.somalier', checkIfExists: true), + file(params.modules_testdata_base_path + 'delete_me/somalier/tumour.somalier', checkIfExists: true) + ], + file(params.modules_testdata_base_path + 'delete_me/somalier/family.ped', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'delete_me/somalier/groups.txt', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("[ delete_me, [] ], [] -stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'cohort', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'delete_me/somalier/normal.somalier', checkIfExists: true), + file(params.modules_testdata_base_path + 'delete_me/somalier/tumour.somalier', checkIfExists: true) + ], + [] + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("[ delete_me, ped ], groups -stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'cohort', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'delete_me/somalier/normal.somalier', checkIfExists: true), + file(params.modules_testdata_base_path + 'delete_me/somalier/tumour.somalier', checkIfExists: true) + ], + file(params.modules_testdata_base_path + 'delete_me/somalier/family.ped', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'delete_me/somalier/groups.txt', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/somalier/relate/tests/main.nf.test.snap b/modules/nf-core/somalier/relate/tests/main.nf.test.snap new file mode 100644 index 00000000..54a73033 --- /dev/null +++ b/modules/nf-core/somalier/relate/tests/main.nf.test.snap @@ -0,0 +1,286 @@ +{ + "[ delete_me, [] ], []": { + "content": [ + { + "0": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.html:md5,03cac9b2c67a8a06f63e07f83ee11e18" + ] + ], + "1": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.pairs.tsv:md5,54d1e9fca1bf9d747d4254c6fa98edcf" + ] + ], + "2": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.samples.tsv:md5,97257d88886db1325c4d7d10cefa7169" + ] + ], + "3": [ + "versions.yml:md5,59d805a9f89558414535c136c814bea6" + ], + "html": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.html:md5,03cac9b2c67a8a06f63e07f83ee11e18" + ] + ], + "pairs_tsv": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.pairs.tsv:md5,54d1e9fca1bf9d747d4254c6fa98edcf" + ] + ], + "samples_tsv": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.samples.tsv:md5,97257d88886db1325c4d7d10cefa7169" + ] + ], + "versions": [ + "versions.yml:md5,59d805a9f89558414535c136c814bea6" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-02T05:29:21.162582556" + }, + "[ delete_me, [] ], [] -stub": { + "content": [ + { + "0": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.pairs.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.samples.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,59d805a9f89558414535c136c814bea6" + ], + "html": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "pairs_tsv": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.pairs.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "samples_tsv": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.samples.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,59d805a9f89558414535c136c814bea6" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-02T05:29:43.887124223" + }, + "[ delete_me, ped ], groups -stub": { + "content": [ + { + "0": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.pairs.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.samples.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,59d805a9f89558414535c136c814bea6" + ], + "html": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "pairs_tsv": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.pairs.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "samples_tsv": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.samples.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,59d805a9f89558414535c136c814bea6" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-02T05:29:55.034913513" + }, + "[ delete_me, ped ], groups": { + "content": [ + { + "0": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.html:md5,0d573016c9279ccdfdcfd4eb01d73b89" + ] + ], + "1": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.pairs.tsv:md5,8655714f1e5359329188e9f501168131" + ] + ], + "2": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.samples.tsv:md5,38ef93340e55fbeef47640abda9e48b0" + ] + ], + "3": [ + "versions.yml:md5,59d805a9f89558414535c136c814bea6" + ], + "html": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.html:md5,0d573016c9279ccdfdcfd4eb01d73b89" + ] + ], + "pairs_tsv": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.pairs.tsv:md5,8655714f1e5359329188e9f501168131" + ] + ], + "samples_tsv": [ + [ + { + "id": "cohort", + "single_end": false + }, + "cohort.samples.tsv:md5,38ef93340e55fbeef47640abda9e48b0" + ] + ], + "versions": [ + "versions.yml:md5,59d805a9f89558414535c136c814bea6" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-02T05:29:32.451456985" + } +} \ No newline at end of file diff --git a/modules/nf-core/somalier/relate/tests/tags.yml b/modules/nf-core/somalier/relate/tests/tags.yml new file mode 100644 index 00000000..c80de730 --- /dev/null +++ b/modules/nf-core/somalier/relate/tests/tags.yml @@ -0,0 +1,2 @@ +somalier/relate: + - "modules/nf-core/somalier/relate/**" diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml index 4fe40c56..56cc0fb1 100644 --- a/modules/nf-core/tabix/bgzip/environment.yml +++ b/modules/nf-core/tabix/bgzip/environment.yml @@ -5,3 +5,4 @@ channels: - defaults dependencies: - bioconda::tabix=1.11 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf index 7772e9ad..67991c74 100644 --- a/modules/nf-core/tabix/bgzip/main.nf +++ b/modules/nf-core/tabix/bgzip/main.nf @@ -4,8 +4,8 @@ process TABIX_BGZIP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'biocontainers/tabix:1.11--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : + 'biocontainers/htslib:1.20--h5efdd21_2' }" input: tuple val(meta), path(input) @@ -44,7 +44,8 @@ process TABIX_BGZIP { output = in_bgzip ? input.getBaseName() : "${prefix}.${input.getExtension()}.gz" """ - touch ${output} + echo "" | gzip > ${output} + touch ${output}.gzi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config b/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config new file mode 100644 index 00000000..6b6ff55f --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/bgzip_compress.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIP { + ext.args = ' -i' + } +} diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test b/modules/nf-core/tabix/bgzip/tests/main.nf.test new file mode 100644 index 00000000..d784aa07 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test @@ -0,0 +1,111 @@ +nextflow_process { + + name "Test Process TABIX_BGZIP" + script "modules/nf-core/tabix/bgzip/main.nf" + process "TABIX_BGZIP" + + tag "modules" + tag "modules_nfcore" + tag "tabix" + tag "tabix/bgzip" + + test("sarscov2_vcf_bgzip_compress") { + when { + process { + """ + input[0] = [ + [ id:'bgzip_test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.output[0][1]).name + ).match("bgzip_test") + } + ) + } + } + + test("homo_genome_bedgz_compress") { + when { + process { + """ + input[0] = [ + [ id:'bedgz_test' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.output[0][1]).name + ).match("bedgz_test") + } + ) + } + } + + test("sarscov2_vcf_bgzip_compress_stub") { + options '-stub' + config "./bgzip_compress.config" + + when { + process { + """ + input[0] = [ + [ id:"test_stub" ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.output[0][1]).name + ).match("test_stub") + } + ) + } + } + + test("sarscov2_vcf_bgzip_compress_gzi") { + config "./bgzip_compress.config" + when { + process { + """ + input[0] = [ + [ id:"gzi_compress_test" ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gzi[0][1]).name + ).match("gzi_compress_test") + } + ) + } + } +} diff --git a/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap new file mode 100644 index 00000000..0748143f --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap @@ -0,0 +1,218 @@ +{ + "gzi_compress_test": { + "content": [ + "gzi_compress_test.vcf.gz.gzi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:52:29.328146" + }, + "homo_genome_bedgz_compress": { + "content": [ + { + "0": [ + [ + { + "id": "bedgz_test" + }, + "bedgz_test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ], + "gzi": [ + + ], + "output": [ + [ + { + "id": "bedgz_test" + }, + "bedgz_test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:28:34.159992362" + }, + "test_stub": { + "content": [ + "test_stub.vcf.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:52:20.811489" + }, + "sarscov2_vcf_bgzip_compress": { + "content": [ + { + "0": [ + [ + { + "id": "bgzip_test" + }, + "bgzip_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ], + "gzi": [ + + ], + "output": [ + [ + { + "id": "bgzip_test" + }, + "bgzip_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "versions": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:28:22.087769106" + }, + "sarscov2_vcf_bgzip_compress_gzi": { + "content": [ + { + "0": [ + [ + { + "id": "gzi_compress_test" + }, + "gzi_compress_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "1": [ + [ + { + "id": "gzi_compress_test" + }, + "gzi_compress_test.vcf.gz.gzi:md5,26fd00d4e26141cd11561f6e7d4a2ad0" + ] + ], + "2": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ], + "gzi": [ + [ + { + "id": "gzi_compress_test" + }, + "gzi_compress_test.vcf.gz.gzi:md5,26fd00d4e26141cd11561f6e7d4a2ad0" + ] + ], + "output": [ + [ + { + "id": "gzi_compress_test" + }, + "gzi_compress_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "versions": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:28:57.15091665" + }, + "bgzip_test": { + "content": [ + "bgzip_test.vcf.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:52:03.768295" + }, + "bedgz_test": { + "content": [ + "bedgz_test.bed" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:52:12.453855" + }, + "sarscov2_vcf_bgzip_compress_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test_stub" + }, + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test_stub" + }, + "test_stub.vcf.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ], + "gzi": [ + [ + { + "id": "test_stub" + }, + "test_stub.vcf.gz.gzi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "output": [ + [ + { + "id": "test_stub" + }, + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,753c29916d45debdde52f4ac7c745f61" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:28:45.219404786" + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/bgzip/tests/tags.yml b/modules/nf-core/tabix/bgzip/tests/tags.yml new file mode 100644 index 00000000..de0eec86 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/tags.yml @@ -0,0 +1,2 @@ +tabix/bgzip: + - "modules/nf-core/tabix/bgzip/**" diff --git a/modules/nf-core/tabix/bgzip/tests/vcf_none.config b/modules/nf-core/tabix/bgzip/tests/vcf_none.config new file mode 100644 index 00000000..f3a3c467 --- /dev/null +++ b/modules/nf-core/tabix/bgzip/tests/vcf_none.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIP { + ext.args = '' + } +} diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml index 028461c9..b9644de9 100644 --- a/modules/nf-core/tabix/bgziptabix/environment.yml +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -5,3 +5,4 @@ channels: - defaults dependencies: - bioconda::tabix=1.11 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index f9482690..05041f49 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -4,8 +4,8 @@ process TABIX_BGZIPTABIX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'biocontainers/tabix:1.11--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : + 'biocontainers/htslib:1.20--h5efdd21_2' }" input: tuple val(meta), path(input) @@ -24,7 +24,7 @@ process TABIX_BGZIPTABIX { def prefix = task.ext.prefix ?: "${meta.id}" """ bgzip --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz - tabix $args2 ${prefix}.${input.getExtension()}.gz + tabix --threads ${task.cpus} $args2 ${prefix}.${input.getExtension()}.gz cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -35,7 +35,7 @@ process TABIX_BGZIPTABIX { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.${input.getExtension()}.gz + echo "" | gzip > ${prefix}.${input.getExtension()}.gz touch ${prefix}.${input.getExtension()}.gz.tbi touch ${prefix}.${input.getExtension()}.gz.csi diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test new file mode 100644 index 00000000..1a84d74f --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test @@ -0,0 +1,94 @@ +nextflow_process { + + name "Test Process TABIX_BGZIPTABIX" + script "modules/nf-core/tabix/bgziptabix/main.nf" + process "TABIX_BGZIPTABIX" + + tag "modules" + tag "modules_nfcore" + tag "tabix" + tag "tabix/bgziptabix" + + test("sarscov2_bed_tbi") { + config "./tabix_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'tbi_test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gz_tbi[0][1]).name + ).match("tbi_test") + } + ) + } + } + + test("sarscov2_bed_csi") { + config "./tabix_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'csi_test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gz_csi[0][1]).name + ).match("csi_test") + } + ) + } + + } + + test("sarscov2_bed_csi_stub") { + config "./tabix_csi.config" + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gz_csi[0][1]).name + ).match("csi_stub") + } + ) + } + + } + +} diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap new file mode 100644 index 00000000..c166ea72 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap @@ -0,0 +1,167 @@ +{ + "sarscov2_bed_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_test" + }, + "tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", + "tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ], + "gz_csi": [ + + ], + "gz_tbi": [ + [ + { + "id": "tbi_test" + }, + "tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", + "tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c" + ] + ], + "versions": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:29:16.053817543" + }, + "sarscov2_bed_csi": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "csi_test" + }, + "csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", + "csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5" + ] + ], + "2": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ], + "gz_csi": [ + [ + { + "id": "csi_test" + }, + "csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", + "csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5" + ] + ], + "gz_tbi": [ + + ], + "versions": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:29:27.667745444" + }, + "csi_test": { + "content": [ + "csi_test.bed.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:51:00.548801" + }, + "csi_stub": { + "content": [ + "test.bed.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:51:09.218454" + }, + "tbi_test": { + "content": [ + "tbi_test.bed.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-02-19T14:50:51.579654" + }, + "sarscov2_bed_csi_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ], + "gz_csi": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gz_tbi": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:29:45.105209991" + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config b/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config new file mode 100644 index 00000000..fb41a314 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIPTABIX { + ext.args2 = '-p vcf --csi' + } +} diff --git a/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config b/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config new file mode 100644 index 00000000..c1915dc4 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIPTABIX { + ext.args2 = '-p vcf' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/bgziptabix/tests/tags.yml b/modules/nf-core/tabix/bgziptabix/tests/tags.yml new file mode 100644 index 00000000..5052b4d7 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/tags.yml @@ -0,0 +1,2 @@ +tabix/bgziptabix: + - "modules/nf-core/tabix/bgziptabix/**" diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index 7167fb87..4d1f9dd4 100644 --- a/modules/nf-core/tabix/tabix/environment.yml +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -1,7 +1,10 @@ name: tabix_tabix + channels: - conda-forge - bioconda - defaults + dependencies: + - bioconda::htslib=1.20 - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index c304a8a3..13acd670 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -4,8 +4,8 @@ process TABIX_TABIX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'biocontainers/tabix:1.11--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : + 'biocontainers/htslib:1.20--h5efdd21_2' }" input: tuple val(meta), path(tab) @@ -21,7 +21,10 @@ process TABIX_TABIX { script: def args = task.ext.args ?: '' """ - tabix $args $tab + tabix \\ + --threads $task.cpus \\ + $args \\ + $tab cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -30,11 +33,11 @@ process TABIX_TABIX { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${tab}.tbi - cat <<-END_VERSIONS > versions.yml + touch ${tab}.csi + cat <<-END_VERSIONS > versions.yml "${task.process}": tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test new file mode 100644 index 00000000..102b0d7b --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test @@ -0,0 +1,136 @@ +nextflow_process { + + name "Test Process TABIX_TABIX" + script "modules/nf-core/tabix/tabix/main.nf" + process "TABIX_TABIX" + + tag "modules" + tag "modules_nfcore" + tag "tabix" + tag "tabix/tabix" + + test("sarscov2_bedgz_tbi") { + config "./tabix_bed.config" + when { + process { + """ + input[0] = [ + [ id:'tbi_bed' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.tbi[0][1]).name + ).match() } + ) + } + } + + test("sarscov2_gff_tbi") { + config "./tabix_gff.config" + when { + process { + """ + input[0] = [ + [ id:'tbi_gff' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.tbi[0][1]).name).match() } + ) + } + + } + + test("sarscov2_vcf_tbi") { + config "./tabix_vcf_tbi.config" + when { + process { + """ + input[0] = [ + [ id:'tbi_vcf' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.tbi[0][1]).name + ).match() } + ) + } + + } + + test("sarscov2_vcf_csi") { + config "./tabix_vcf_csi.config" + when { + process { + """ + input[0] = [ + [ id:'vcf_csi' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.csi[0][1]).name + ).match() } + ) + } + + } + + test("sarscov2_vcf_csi_stub") { + config "./tabix_vcf_csi.config" + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'vcf_csi_stub' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out, + file(process.out.csi[0][1]).name + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap new file mode 100644 index 00000000..c2b9ed0b --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap @@ -0,0 +1,212 @@ +{ + "sarscov2_gff_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_gff" + }, + "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "tbi_gff" + }, + "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926" + ] + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "genome.gff3.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:25.653807564" + }, + "sarscov2_bedgz_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_bed" + }, + "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "tbi_bed" + }, + "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d" + ] + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "test.bed.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:09.754082161" + }, + "sarscov2_vcf_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_vcf" + }, + "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "tbi_vcf" + }, + "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e" + ] + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "test.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:40.042648294" + }, + "sarscov2_vcf_csi_stub": { + "content": [ + { + "0": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "test.vcf.gz.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:07:08.700367261" + }, + "sarscov2_vcf_csi": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "vcf_csi" + }, + "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b" + ] + ], + "2": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ], + "csi": [ + [ + { + "id": "vcf_csi" + }, + "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b" + ] + ], + "tbi": [ + + ], + "versions": [ + "versions.yml:md5,07064637fb8a217174052be8e40234e2" + ] + }, + "test.vcf.gz.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:55.362067748" + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_bed.config b/modules/nf-core/tabix/tabix/tests/tabix_bed.config new file mode 100644 index 00000000..7ff05905 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_bed.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p bed' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_gff.config b/modules/nf-core/tabix/tabix/tests/tabix_gff.config new file mode 100644 index 00000000..20c0a1e3 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_gff.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p gff' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config new file mode 100644 index 00000000..eb4f2d7e --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p vcf --csi' + } +} diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config new file mode 100644 index 00000000..2774c8a9 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p vcf' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tags.yml b/modules/nf-core/tabix/tabix/tests/tags.yml new file mode 100644 index 00000000..6eda0653 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tags.yml @@ -0,0 +1,2 @@ +tabix/tabix: + - "modules/nf-core/tabix/tabix/**" diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 0c9cbb10..4f498244 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,11 +1,9 @@ name: untar - channels: - conda-forge - bioconda - defaults - dependencies: - conda-forge::grep=3.11 - - conda-forge::sed=4.7 + - conda-forge::sed=4.8 - conda-forge::tar=1.34 diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 8a75bb95..9bd8f554 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -4,8 +4,8 @@ process UNTAR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : + 'nf-core/ubuntu:22.04' }" input: tuple val(meta), path(archive) @@ -52,8 +52,29 @@ process UNTAR { stub: prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, "")) """ - mkdir $prefix - touch ${prefix}/file.txt + mkdir ${prefix} + ## Dry-run untaring the archive to get the files and place all in prefix + if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then + for i in `tar -tf ${archive}`; + do + if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]]; + then + touch \${i} + else + mkdir -p \${i} + fi + done + else + for i in `tar -tf ${archive}`; + do + if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]]; + then + touch ${prefix}/\${i} + else + mkdir -p ${prefix}/\${i} + fi + done + fi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test index 2a7c97bf..c957517a 100644 --- a/modules/nf-core/untar/tests/main.nf.test +++ b/modules/nf-core/untar/tests/main.nf.test @@ -6,6 +6,7 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "untar" + test("test_untar") { when { @@ -19,10 +20,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.untar).match("test_untar") }, + { assert snapshot(process.out).match() }, ) } - } test("test_untar_onlyfiles") { @@ -38,10 +38,48 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.untar).match("test_untar_onlyfiles") }, + { assert snapshot(process.out).match() }, ) } + } + + test("test_untar - stub") { + + options "-stub" + when { + process { + """ + input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } } + test("test_untar_onlyfiles - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + } } diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap index 64550292..ceb91b79 100644 --- a/modules/nf-core/untar/tests/main.nf.test.snap +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -1,42 +1,158 @@ { "test_untar_onlyfiles": { "content": [ - [ - [ + { + "0": [ [ - - ], + [ + + ], + [ + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ + [ + [ + + ], + [ + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-10T12:04:28.231047" + }, + "test_untar_onlyfiles - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ [ - "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + [ + + ], + [ + "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] - ] + } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-02-28T11:49:41.320643" + "timestamp": "2024-07-10T12:04:45.773103" + }, + "test_untar - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ + [ + [ + + ], + [ + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-10T12:04:36.777441" }, "test_untar": { "content": [ - [ - [ + { + "0": [ [ - - ], + [ + + ], + [ + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ [ - "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", - "opts.k2d:md5,a033d00cf6759407010b21700938f543", - "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + [ + + ], + [ + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + ] ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] - ] + } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-02-28T11:49:33.795172" + "timestamp": "2024-07-10T12:04:19.377674" } } \ No newline at end of file diff --git a/modules/nf-core/vardictjava/environment.yml b/modules/nf-core/vardictjava/environment.yml index 92d169fd..4e8905e5 100644 --- a/modules/nf-core/vardictjava/environment.yml +++ b/modules/nf-core/vardictjava/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: + - bioconda::htslib=1.20 - bioconda::vardict-java=1.8.3 diff --git a/modules/nf-core/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf index 50d7dfab..6329391c 100644 --- a/modules/nf-core/vardictjava/main.nf +++ b/modules/nf-core/vardictjava/main.nf @@ -4,8 +4,8 @@ process VARDICTJAVA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/vardict-java:1.8.3--hdfd78af_0': - 'biocontainers/vardict-java:1.8.3--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-731b8c4cf44d76e9aa181af565b9eee448d82a8c:edd70e76f3529411a748168f6eb1a61f29702123-0' : + 'biocontainers/mulled-v2-731b8c4cf44d76e9aa181af565b9eee448d82a8c:edd70e76f3529411a748168f6eb1a61f29702123-0' }" input: tuple val(meta), path(bams), path(bais), path(bed) @@ -13,7 +13,7 @@ process VARDICTJAVA { tuple val(meta3), path(fasta_fai) output: - tuple val(meta), path("*.vcf"), emit: vcf + tuple val(meta), path("*.vcf.gz"), emit: vcf path "versions.yml" , emit: versions when: @@ -22,9 +22,10 @@ process VARDICTJAVA { script: def args = task.ext.args ?: '-c 1 -S 2 -E 3' def args2 = task.ext.args2 ?: '' + def args3 = task.ext.args3 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def somatic = bams instanceof ArrayList && bams.size() == 2 ? true : false + def somatic = bams instanceof List && bams.size() == 2 ? true : false def input = somatic ? "-b \"${bams[0]}|${bams[1]}\"" : "-b ${bams}" def filter = somatic ? "testsomatic.R" : "teststrandbias.R" def convert_to_vcf = somatic ? "var2vcf_paired.pl" : "var2vcf_valid.pl" @@ -39,8 +40,7 @@ process VARDICTJAVA { | ${filter} \\ | ${convert_to_vcf} \\ ${args2} \\ - | sed -e 's/##FORMAT= ${prefix}.vcf + | bgzip ${args3} --threads ${task.cpus} > ${prefix}.vcf.gz cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -52,10 +52,11 @@ process VARDICTJAVA { stub: def args = task.ext.args ?: '-c 1 -S 2 -E 3' def args2 = task.ext.args2 ?: '' + def args3 = task.ext.args3 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf + echo '' | gzip > ${prefix}.vcf.gz cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/vardictjava/meta.yml b/modules/nf-core/vardictjava/meta.yml index 657d1531..5c2fc921 100644 --- a/modules/nf-core/vardictjava/meta.yml +++ b/modules/nf-core/vardictjava/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://github.com/AstraZeneca-NGS/VarDictJava" tool_dev_url: "https://github.com/AstraZeneca-NGS/VarDictJava" doi: "10.1093/nar/gkw227 " - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/vardictjava/tests/main.nf.test b/modules/nf-core/vardictjava/tests/main.nf.test index 483a753a..8e5fec10 100644 --- a/modules/nf-core/vardictjava/tests/main.nf.test +++ b/modules/nf-core/vardictjava/tests/main.nf.test @@ -17,17 +17,17 @@ nextflow_process { """ input[0] = Channel.value([ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ]) input[1] = [ [id:"ref"], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [id:"ref"], - file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] """ } @@ -55,22 +55,22 @@ nextflow_process { input[0] = Channel.value([ [ id:'test' ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) ], [ - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai', checkIfExists: true) ], - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ]) input[1] = [ [id:"ref"], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] input[2] = [ [id:"ref"], - file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] """ } diff --git a/modules/nf-core/vardictjava/tests/main.nf.test.snap b/modules/nf-core/vardictjava/tests/main.nf.test.snap index 4ccb63ec..c32a68b7 100644 --- a/modules/nf-core/vardictjava/tests/main.nf.test.snap +++ b/modules/nf-core/vardictjava/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "test.vcf:md5,e8411ecae49b4f6afa6ea0b681ea506e" + "test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e" ] ], "1": [ @@ -18,7 +18,7 @@ { "id": "test" }, - "test.vcf:md5,e8411ecae49b4f6afa6ea0b681ea506e" + "test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e" ] ], "versions": [ @@ -26,7 +26,11 @@ ] } ], - "timestamp": "2023-10-24T09:24:20.923172332" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-04T19:08:38.328190023" }, "homo_sapiens - [[bam, bam], [bai, bai], bed] - fasta - fai": { "content": [ @@ -36,7 +40,7 @@ { "id": "test" }, - "test.vcf:md5,8acdd8ca041f024aab55d102fb6b0c38" + "test.vcf.gz:md5,b52c874c18be636d876d1e0df4a449c3" ] ], "1": [ @@ -47,7 +51,7 @@ { "id": "test" }, - "test.vcf:md5,8acdd8ca041f024aab55d102fb6b0c38" + "test.vcf.gz:md5,b52c874c18be636d876d1e0df4a449c3" ] ], "versions": [ @@ -55,6 +59,10 @@ ] } ], - "timestamp": "2023-10-24T09:24:29.462707023" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-04T19:08:54.416661915" } } \ No newline at end of file diff --git a/modules/nf-core/vardictjava/vardictjava.diff b/modules/nf-core/vardictjava/vardictjava.diff deleted file mode 100644 index 0efca40b..00000000 --- a/modules/nf-core/vardictjava/vardictjava.diff +++ /dev/null @@ -1,13 +0,0 @@ -Changes in module 'nf-core/vardictjava' ---- modules/nf-core/vardictjava/main.nf -+++ modules/nf-core/vardictjava/main.nf -@@ -39,6 +39,7 @@ - | ${filter} \\ - | ${convert_to_vcf} \\ - ${args2} \\ -+ | sed -e 's/##FORMAT= ${prefix}.vcf - - cat <<-END_VERSIONS > versions.yml - -************************************************************ diff --git a/modules/nf-core/vcf2db/Dockerfile b/modules/nf-core/vcf2db/Dockerfile deleted file mode 100644 index b271f667..00000000 --- a/modules/nf-core/vcf2db/Dockerfile +++ /dev/null @@ -1,11 +0,0 @@ -FROM mambaorg/micromamba:1.4-focal - -COPY ./vcf2db_env.yaml . - -RUN micromamba update --file ./vcf2db_env.yaml --yes -RUN micromamba install --yes --name base --no-deps -c bioconda vcf2db==2020.02.24 -RUN micromamba install --yes --name base --no-deps -c conda-forge coreutils -RUN micromamba clean --all --yes - -ARG MAMBA_DOCKERFILE_ACTIVATE=1 -ENV PATH "$MAMBA_ROOT_PREFIX/bin:$PATH" \ No newline at end of file diff --git a/modules/nf-core/vcf2db/main.nf b/modules/nf-core/vcf2db/main.nf index 85180a37..56c26bb6 100644 --- a/modules/nf-core/vcf2db/main.nf +++ b/modules/nf-core/vcf2db/main.nf @@ -4,7 +4,9 @@ process VCF2DB { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" - container "cmgg/vcf2db:2020.02.24" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/vcf2db:2020.02.24--pl5321hdfd78af_3': + 'biocontainers/vcf2db:2020.02.24--pl5321hdfd78af_3' }" input: tuple val(meta), path(vcf), path(ped) @@ -27,12 +29,6 @@ process VCF2DB { ${prefix}.db \\ $args - sqlite3 ${prefix}.db 'CREATE INDEX idx_variant_impacts_id ON variant_impacts (variant_id)' && \\ - sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN tags varchar(255)' && \\ - sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN tags_user varchar(255)' && \\ - sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN notes varchar(255)' && \\ - sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN notes_user varchar(255)' - cat <<-END_VERSIONS > versions.yml "${task.process}": vcf2db: $VERSION diff --git a/modules/nf-core/vcf2db/tests/main.nf.test b/modules/nf-core/vcf2db/tests/main.nf.test index 52742adf..9532b432 100644 --- a/modules/nf-core/vcf2db/tests/main.nf.test +++ b/modules/nf-core/vcf2db/tests/main.nf.test @@ -15,8 +15,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true) ] """ } @@ -25,7 +25,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + file(process.out.db[0][1]).name, // Conda test fails with content md5 + process.out.versions + ).match() + } ) } @@ -40,8 +44,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['genome']['justhusky_minimal_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['justhusky_ped'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/ped/justhusky.ped', checkIfExists: true) ] """ } diff --git a/modules/nf-core/vcf2db/tests/main.nf.test.snap b/modules/nf-core/vcf2db/tests/main.nf.test.snap index c51bea34..5e29c6ba 100644 --- a/modules/nf-core/vcf2db/tests/main.nf.test.snap +++ b/modules/nf-core/vcf2db/tests/main.nf.test.snap @@ -28,37 +28,23 @@ ] } ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, "timestamp": "2024-01-10T16:13:32.293507403" }, "homo_sapiens - vcf, ped": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.db:md5,0766bacb306d642a8358b375c4c1836f" - ] - ], - "1": [ - "versions.yml:md5,3d9eedf7998cb77b614736659eb22b1d" - ], - "db": [ - [ - { - "id": "test", - "single_end": false - }, - "test.db:md5,0766bacb306d642a8358b375c4c1836f" - ] - ], - "versions": [ - "versions.yml:md5,3d9eedf7998cb77b614736659eb22b1d" - ] - } + "test.db", + [ + "versions.yml:md5,3d9eedf7998cb77b614736659eb22b1d" + ] ], - "timestamp": "2024-01-10T16:13:25.722991475" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-08-06T10:27:06.932652" } } \ No newline at end of file diff --git a/modules/nf-core/vcf2db/vcf2db.diff b/modules/nf-core/vcf2db/vcf2db.diff deleted file mode 100644 index 00fc493f..00000000 --- a/modules/nf-core/vcf2db/vcf2db.diff +++ /dev/null @@ -1,143 +0,0 @@ -Changes in module 'nf-core/vcf2db' ---- modules/nf-core/vcf2db/main.nf -+++ modules/nf-core/vcf2db/main.nf -@@ -4,9 +4,7 @@ - - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "${moduleDir}/environment.yml" -- container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -- 'https://depot.galaxyproject.org/singularity/vcf2db:2020.02.24--pl5321hdfd78af_3': -- 'biocontainers/vcf2db:2020.02.24--pl5321hdfd78af_3' }" -+ container "cmgg/vcf2db:2020.02.24" - - input: - tuple val(meta), path(vcf), path(ped) -@@ -29,6 +27,12 @@ - ${prefix}.db \\ - $args - -+ sqlite3 ${prefix}.db 'CREATE INDEX idx_variant_impacts_id ON variant_impacts (variant_id)' && \\ -+ sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN tags varchar(255)' && \\ -+ sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN tags_user varchar(255)' && \\ -+ sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN notes varchar(255)' && \\ -+ sqlite3 ${prefix}.db 'ALTER TABLE variants ADD COLUMN notes_user varchar(255)' -+ - cat <<-END_VERSIONS > versions.yml - "${task.process}": - vcf2db: $VERSION - ---- /dev/null -+++ modules/nf-core/vcf2db/vcf2db_env.yaml -@@ -0,0 +1,96 @@ -+name: base -+channels: -+ - conda-forge -+ - bioconda -+ - defaults -+dependencies: -+ - _libgcc_mutex=0.1=conda_forge -+ - _openmp_mutex=4.5=1_llvm -+ - backports=1.0=py27_1 -+ - backports.functools_lru_cache=1.6.1=pyhd3eb1b0_0 -+ - backports.shutil_get_terminal_size=1.0.0=py27_2 -+ - backports_abc=0.5=py27_0 -+ - backports.functools_lru_cache=1.6.1=pyhd3eb1b0_0 -+ - backports_abc=0.5=py27_0 -+ - blas=2.17=openblas -+ - bzip2=1.0.8=h516909a_3 -+ - c-ares=1.17.1=h36c2ea0_0 -+ - ca-certificates=2020.11.8=ha878542_0 -+ - certifi=2016.9.26=py27_0 -+ - click=7.1.2=pyh9f0ad1d_0 -+ - coloredlogs=14.0=py27h8c360ce_1 -+ - cycler=0.10.0=py27_0 -+ - cyvcf2=0.20.9=py27h22a6d1c_0 -+ - decorator=4.4.2=py_0 -+ - freetype=2.10.4=he06d7ca_0 -+ - functools32=3.2.3.2=py27_2 -+ - futures=3.3.0=py27h8c360ce_1 -+ - geneimpacts=0.3.7=py27_0 -+ - htslib=1.10.2=hd3b49d5_1 -+ - humanfriendly=8.1=py27h8c360ce_1 -+ - icu=58.2=hf484d3e_1000 -+ - kiwisolver=1.1.0=py27h9e3301b_1 -+ - krb5=1.17.2=h926e7f8_0 -+ - libblas=3.8.0=17_openblas -+ - libcblas=3.8.0=17_openblas -+ - libcurl=7.71.1=hcdd3856_8 -+ - libdeflate=1.6=h516909a_0 -+ - libedit=3.1.20191231=he28a2e2_2 -+ - libev=4.33=h516909a_1 -+ - libffi=3.3=he6710b0_2 -+ - libgcc-ng=9.3.0=h5dbcf3e_17 -+ - libgfortran-ng=7.5.0=hae1eefd_17 -+ - libgfortran4=7.5.0=hae1eefd_17 -+ - liblapack=3.8.0=17_openblas -+ - liblapacke=3.8.0=17_openblas -+ - liblapacke=3.8.0=17_openblas -+ - libnghttp2=1.41.0=hf8bcb03_2 -+ - libopenblas=0.3.10=pthreads_hb3c22a3_5 -+ - libpng=1.6.37=hed695b0_2 -+ - libssh2=1.9.0=hab1572f_5 -+ - libstdcxx-ng=9.3.0=h2ae2ef3_17 -+ - llvm-openmp=11.0.0=hfc4b9b4_1 -+ - matplotlib-base=2.2.4=py27hfd891ef_0 -+ - monotonic=1.5=py_0 -+ - ncurses=6.2=h58526e2_4 -+ - networkx=2.2=py27_1 -+ - nomkl=3.0=0 -+ - numpy=1.16.6=py27h30dfecb_0 -+ - numpy-base=1.16.6=py27h2f8d375_0 -+ - numpy-base=1.16.6=py27h2f8d375_0 -+ - openssl=1.1.1h=h516909a_0 -+ - pandas=0.24.2=py27hf484d3e_0 -+ - pathlib2=2.3.5=py27h8c360ce_1 -+ - patsy=0.5.1=py27_0 -+ - peddy=0.4.7=pyh864c0ab_0 -+ - pip=20.1.1=pyh9f0ad1d_0 -+ - pyparsing=2.4.7=pyh9f0ad1d_0 -+ - python=2.7.18=h15b4118_1 -+ - python-dateutil=2.8.1=py_0 -+ - python-lzo=1.12=py27h42e1302_1001 -+ - python-snappy=0.5.4=py27hee44bf9_1 -+ - python_abi=2.7=1_cp27mu -+ - python-dateutil=2.8.1=py_0 -+ - python-snappy=0.5.4=py27hee44bf9_1 -+ - python_abi=2.7=1_cp27mu -+ - pytz=2020.1=pyh9f0ad1d_0 -+ - readline=8.0=he28a2e2_2 -+ - scandir=1.10.0=py27hdf8410d_1 -+ - scikit-learn=0.20.3=py27ha8026db_1 -+ - scipy=1.2.1=py27h921218d_2 -+ - seaborn=0.9.0=py27_0 -+ - setuptools=44.0.0=py27_0 -+ - singledispatch=3.4.0.3=py27_1000 -+ - six=1.15.0=pyh9f0ad1d_0 -+ - snappy=1.1.8=he1b5a44_3 -+ - sqlalchemy=1.3.15=py27hdf8410d_1 -+ - sqlite=3.33.0=h4cf870e_1 -+ - statsmodels=0.10.2=py27hc1659b7_0 -+ - subprocess32=3.5.4=py27h516909a_0 -+ - tk=8.6.10=hed695b0_1 -+ - toolshed=0.4.6=py27_0 -+ - tornado=5.1.1=py27h14c3975_1000 -+ - wheel=0.35.1=pyh9f0ad1d_0 -+ - xz=5.2.5=h516909a_1 -+ - zlib=1.2.11=h516909a_1010 -+ - zstd=1.4.5=h6597ccf_2 - ---- /dev/null -+++ modules/nf-core/vcf2db/Dockerfile -@@ -0,0 +1,11 @@ -+FROM mambaorg/micromamba:1.4-focal -+ -+COPY ./vcf2db_env.yaml . -+ -+RUN micromamba update --file ./vcf2db_env.yaml --yes -+RUN micromamba install --yes --name base --no-deps -c bioconda vcf2db==2020.02.24 -+RUN micromamba install --yes --name base --no-deps -c conda-forge coreutils -+RUN micromamba clean --all --yes -+ -+ARG MAMBA_DOCKERFILE_ACTIVATE=1 -+ENV PATH "$MAMBA_ROOT_PREFIX/bin:$PATH" -************************************************************ diff --git a/modules/nf-core/vcf2db/vcf2db_env.yaml b/modules/nf-core/vcf2db/vcf2db_env.yaml deleted file mode 100644 index 1cfa95f8..00000000 --- a/modules/nf-core/vcf2db/vcf2db_env.yaml +++ /dev/null @@ -1,96 +0,0 @@ -name: base -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - _libgcc_mutex=0.1=conda_forge - - _openmp_mutex=4.5=1_llvm - - backports=1.0=py27_1 - - backports.functools_lru_cache=1.6.1=pyhd3eb1b0_0 - - backports.shutil_get_terminal_size=1.0.0=py27_2 - - backports_abc=0.5=py27_0 - - backports.functools_lru_cache=1.6.1=pyhd3eb1b0_0 - - backports_abc=0.5=py27_0 - - blas=2.17=openblas - - bzip2=1.0.8=h516909a_3 - - c-ares=1.17.1=h36c2ea0_0 - - ca-certificates=2020.11.8=ha878542_0 - - certifi=2016.9.26=py27_0 - - click=7.1.2=pyh9f0ad1d_0 - - coloredlogs=14.0=py27h8c360ce_1 - - cycler=0.10.0=py27_0 - - cyvcf2=0.20.9=py27h22a6d1c_0 - - decorator=4.4.2=py_0 - - freetype=2.10.4=he06d7ca_0 - - functools32=3.2.3.2=py27_2 - - futures=3.3.0=py27h8c360ce_1 - - geneimpacts=0.3.7=py27_0 - - htslib=1.10.2=hd3b49d5_1 - - humanfriendly=8.1=py27h8c360ce_1 - - icu=58.2=hf484d3e_1000 - - kiwisolver=1.1.0=py27h9e3301b_1 - - krb5=1.17.2=h926e7f8_0 - - libblas=3.8.0=17_openblas - - libcblas=3.8.0=17_openblas - - libcurl=7.71.1=hcdd3856_8 - - libdeflate=1.6=h516909a_0 - - libedit=3.1.20191231=he28a2e2_2 - - libev=4.33=h516909a_1 - - libffi=3.3=he6710b0_2 - - libgcc-ng=9.3.0=h5dbcf3e_17 - - libgfortran-ng=7.5.0=hae1eefd_17 - - libgfortran4=7.5.0=hae1eefd_17 - - liblapack=3.8.0=17_openblas - - liblapacke=3.8.0=17_openblas - - liblapacke=3.8.0=17_openblas - - libnghttp2=1.41.0=hf8bcb03_2 - - libopenblas=0.3.10=pthreads_hb3c22a3_5 - - libpng=1.6.37=hed695b0_2 - - libssh2=1.9.0=hab1572f_5 - - libstdcxx-ng=9.3.0=h2ae2ef3_17 - - llvm-openmp=11.0.0=hfc4b9b4_1 - - matplotlib-base=2.2.4=py27hfd891ef_0 - - monotonic=1.5=py_0 - - ncurses=6.2=h58526e2_4 - - networkx=2.2=py27_1 - - nomkl=3.0=0 - - numpy=1.16.6=py27h30dfecb_0 - - numpy-base=1.16.6=py27h2f8d375_0 - - numpy-base=1.16.6=py27h2f8d375_0 - - openssl=1.1.1h=h516909a_0 - - pandas=0.24.2=py27hf484d3e_0 - - pathlib2=2.3.5=py27h8c360ce_1 - - patsy=0.5.1=py27_0 - - peddy=0.4.7=pyh864c0ab_0 - - pip=20.1.1=pyh9f0ad1d_0 - - pyparsing=2.4.7=pyh9f0ad1d_0 - - python=2.7.18=h15b4118_1 - - python-dateutil=2.8.1=py_0 - - python-lzo=1.12=py27h42e1302_1001 - - python-snappy=0.5.4=py27hee44bf9_1 - - python_abi=2.7=1_cp27mu - - python-dateutil=2.8.1=py_0 - - python-snappy=0.5.4=py27hee44bf9_1 - - python_abi=2.7=1_cp27mu - - pytz=2020.1=pyh9f0ad1d_0 - - readline=8.0=he28a2e2_2 - - scandir=1.10.0=py27hdf8410d_1 - - scikit-learn=0.20.3=py27ha8026db_1 - - scipy=1.2.1=py27h921218d_2 - - seaborn=0.9.0=py27_0 - - setuptools=44.0.0=py27_0 - - singledispatch=3.4.0.3=py27_1000 - - six=1.15.0=pyh9f0ad1d_0 - - snappy=1.1.8=he1b5a44_3 - - sqlalchemy=1.3.15=py27hdf8410d_1 - - sqlite=3.33.0=h4cf870e_1 - - statsmodels=0.10.2=py27hc1659b7_0 - - subprocess32=3.5.4=py27h516909a_0 - - tk=8.6.10=hed695b0_1 - - toolshed=0.4.6=py27_0 - - tornado=5.1.1=py27h14c3975_1000 - - wheel=0.35.1=pyh9f0ad1d_0 - - xz=5.2.5=h516909a_1 - - zlib=1.2.11=h516909a_1010 - - zstd=1.4.5=h6597ccf_2 diff --git a/nextflow.config b/nextflow.config index 12e7effa..46e627fa 100644 --- a/nextflow.config +++ b/nextflow.config @@ -78,9 +78,8 @@ params { // References cmgg_config_base = "/conf/" igenomes_base = null //'s3://ngi-igenomes/igenomes' - igenomes_ignore = true + igenomes_ignore = false genome = "GRCh38" - genomes = [:] genomes_base = "/references/" genomes_ignore = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 34ed7abd..0fc6f59f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -2,7 +2,7 @@ "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-cmgg/germline/master/nextflow_schema.json", "title": "nf-cmgg/germline pipeline parameters", - "description": "A nextflow pipeline for calling and annotating variants", + "description": "A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data", "type": "object", "$defs": { "input_output_options": { @@ -126,13 +126,7 @@ "description": "Do not load the iGenomes reference config.", "fa_icon": "fas fa-ban", "hidden": true, - "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.", - "default": true - }, - "genomes": { - "type": "object", - "description": "A map structure containing the paths to all genome references", - "hidden": true + "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." } }, "required": ["fasta"] diff --git a/subworkflows/local/cram_call_vardictjava/main.nf b/subworkflows/local/cram_call_vardictjava/main.nf index 0475d947..203bdc7c 100644 --- a/subworkflows/local/cram_call_vardictjava/main.nf +++ b/subworkflows/local/cram_call_vardictjava/main.nf @@ -1,6 +1,6 @@ include { SAMTOOLS_CONVERT } from '../../../modules/nf-core/samtools/convert/main' include { VARDICTJAVA } from '../../../modules/nf-core/vardictjava/main' -include { TABIX_BGZIPTABIX as TABIX_SPLIT } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { TABIX_TABIX as TABIX_SPLIT } from '../../../modules/nf-core/tabix/tabix/main' include { TABIX_BGZIPTABIX as TABIX_VCFANNO } from '../../../modules/nf-core/tabix/bgziptabix/main' include { BCFTOOLS_REHEADER } from '../../../modules/nf-core/bcftools/reheader/main' include { VCFANNO } from '../../../modules/nf-core/vcfanno/main' @@ -52,7 +52,7 @@ workflow CRAM_CALL_VARDICTJAVA { .set { ch_vardict_crams } ch_cram_bam.bam - .mix(SAMTOOLS_CONVERT.out.alignment_index) + .mix(SAMTOOLS_CONVERT.out.bam.join(SAMTOOLS_CONVERT.out.bai, failOnMismatch:true, failOnDuplicate:true)) .combine(ch_vardict_crams, by:0) .map { meta, bam, bai, cram, crai, bed, split_count -> def new_meta = meta + [id:bed.baseName, split_count:split_count] @@ -73,13 +73,13 @@ workflow CRAM_CALL_VARDICTJAVA { ch_versions = ch_versions.mix(TABIX_SPLIT.out.versions.first()) VCF_CONCAT_BCFTOOLS( - TABIX_SPLIT.out.gz_tbi, + VARDICTJAVA.out.vcf.join(TABIX_SPLIT.out.tbi, failOnMismatch:true, failOnDuplicate:true), false ) ch_versions = ch_versions.mix(VCF_CONCAT_BCFTOOLS.out.versions) ch_dbsnp_annotated = Channel.empty() - if(ch_dbsnp) { + if(ch_dbsnp != [[],[]]) { ch_dbsnp .map { meta, dbsnp -> [ get_vcfanno_config(dbsnp) ] } .collect() diff --git a/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf b/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf index cf7934a4..8c2a2a41 100644 --- a/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf +++ b/subworkflows/local/gvcf_joint_genotype_gatk4/main.nf @@ -134,9 +134,9 @@ workflow GVCF_JOINT_GENOTYPE_GATK4 { GATK4_GENOTYPEGVCFS( ch_genotypegvcfs_input, - ch_fasta.map { meta, fasta -> fasta }, - ch_fai.map { meta, fai -> fai }, - ch_dict.map { meta, dict -> dict }, + ch_fasta, + ch_fai, + ch_dict, ch_dbsnp, ch_dbsnp_tbi ) diff --git a/subworkflows/local/vcf_extract_relate_somalier/main.nf b/subworkflows/local/vcf_extract_relate_somalier/main.nf index 7b09bbfd..d78e4915 100644 --- a/subworkflows/local/vcf_extract_relate_somalier/main.nf +++ b/subworkflows/local/vcf_extract_relate_somalier/main.nf @@ -4,9 +4,9 @@ include { SOMALIER_RELATE } from '../../../modules/nf-core/somalier/relate/main workflow VCF_EXTRACT_RELATE_SOMALIER { take: ch_vcfs // channel: [mandatory] [ val(meta), path(vcf), path(tbi) ] - ch_fasta // channel: [mandatory] [ path(fasta) ] - ch_fasta_fai // channel: [mandatory] [ path(fai) ] - ch_somalier_sites // channel: [mandatory] [ path(somalier_sites_vcf) ] + ch_fasta // channel: [mandatory] [ val(meta), path(fasta) ] + ch_fasta_fai // channel: [mandatory] [ val(meta), path(fai) ] + ch_somalier_sites // channel: [mandatory] [ val(meta), path(somalier_sites_vcf) ] ch_peds // channel: [mandatory] [ val(meta), path(ped) ] main: diff --git a/subworkflows/local/vcf_validate_small_variants/main.nf b/subworkflows/local/vcf_validate_small_variants/main.nf index 71432d38..eaa17579 100644 --- a/subworkflows/local/vcf_validate_small_variants/main.nf +++ b/subworkflows/local/vcf_validate_small_variants/main.nf @@ -1,6 +1,5 @@ include { RTGTOOLS_VCFEVAL } from '../../../modules/nf-core/rtgtools/vcfeval/main' include { RTGTOOLS_ROCPLOT } from '../../../modules/nf-core/rtgtools/rocplot/main' -include { HAPPY_HAPPY } from '../../../modules/nf-core/happy/happy/main' workflow VCF_VALIDATE_SMALL_VARIANTS { @@ -10,10 +9,6 @@ workflow VCF_VALIDATE_SMALL_VARIANTS { ch_fasta // [happy only] channel: [ meta, fasta ] ch_fasta_fai // [happy only] channel: [ meta, fasta_fai ] ch_vcfeval_sdf // [vcfeval only] channel: [ meta, sdf ] - ch_happy_false_positive_regions // [optional] channel: [ meta, false_positives_bed ] - ch_happy_stratification_tsv // [optional] channel: [ meta, stratification_tsv ] - ch_happy_stratification_beds // [optional] channel: [ meta, [stratification_beds] ] - tools // [mandatory] value: A comma-delimited list of the tools to use for validation (happy,vcfeval,jaccard) main: @@ -51,116 +46,76 @@ workflow VCF_VALIDATE_SMALL_VARIANTS { rtgtools_non_snp_svg_rocplot = Channel.empty() rtgtools_weighted_svg_rocplot = Channel.empty() - val_list_tools = tools.tokenize(",") - ch_input = ch_vcf.join(ch_beds, failOnDuplicate: true, failOnMismatch: true) - if("happy" in val_list_tools){ - ch_happy_input = ch_input - .map { meta, vcf, tbi, truth_vcf, truth_tbi, regions_bed, targets_bed -> - [ meta, vcf, truth_vcf, regions_bed, targets_bed ] + RTGTOOLS_VCFEVAL( + ch_input, + ch_vcfeval_sdf + ) + ch_versions = ch_versions.mix(RTGTOOLS_VCFEVAL.out.versions.first()) + + ch_rocplot_input = RTGTOOLS_VCFEVAL.out.snp_roc + .map { meta, tsv -> + [ meta + [roc_type:'snp'], tsv ] + } + .mix( + RTGTOOLS_VCFEVAL.out.non_snp_roc.map { meta, tsv -> + [ meta + [roc_type:'non_snp'], tsv ] + }, + RTGTOOLS_VCFEVAL.out.weighted_roc.map { meta, tsv -> + [ meta + [roc_type:'weighted'], tsv ] } - HAPPY_HAPPY ( - ch_happy_input, - ch_fasta, - ch_fasta_fai, - ch_happy_false_positive_regions, - ch_happy_stratification_tsv, - ch_happy_stratification_beds - ) - ch_versions = ch_versions.mix(HAPPY_HAPPY.out.versions.first()) - - happy_vcf = HAPPY_HAPPY.out.vcf - happy_tbi = HAPPY_HAPPY.out.tbi - happy_indel_roc = HAPPY_HAPPY.out.roc_indel_locations_csv - happy_indel_roc_pass = HAPPY_HAPPY.out.roc_indel_locations_pass_csv - happy_snp_roc = HAPPY_HAPPY.out.roc_snp_locations_csv - happy_snp_roc_pass = HAPPY_HAPPY.out.roc_snp_locations_pass_csv - happy_roc = HAPPY_HAPPY.out.roc_all_csv - happy_summary = HAPPY_HAPPY.out.summary_csv - happy_extended_csv = HAPPY_HAPPY.out.extended_csv - } - - if("vcfeval" in val_list_tools){ - RTGTOOLS_VCFEVAL( - ch_input, - ch_vcfeval_sdf ) - ch_versions = ch_versions.mix(RTGTOOLS_VCFEVAL.out.versions.first()) - - ch_rocplot_input = RTGTOOLS_VCFEVAL.out.snp_roc - .map { meta, tsv -> - [ meta + [roc_type:'snp'], tsv ] - } - .mix( - RTGTOOLS_VCFEVAL.out.non_snp_roc.map { meta, tsv -> - [ meta + [roc_type:'non_snp'], tsv ] - }, - RTGTOOLS_VCFEVAL.out.weighted_roc.map { meta, tsv -> - [ meta + [roc_type:'weighted'], tsv ] - } - ) - - vcfeval_true_positive_vcf = RTGTOOLS_VCFEVAL.out.tp_vcf - vcfeval_true_positive_vcf_tbi = RTGTOOLS_VCFEVAL.out.tp_tbi - vcfeval_false_negative_vcf = RTGTOOLS_VCFEVAL.out.fn_vcf - vcfeval_false_negative_vcf_tbi = RTGTOOLS_VCFEVAL.out.fn_tbi - vcfeval_false_positive_vcf = RTGTOOLS_VCFEVAL.out.fp_vcf - vcfeval_false_positive_vcf_tbi = RTGTOOLS_VCFEVAL.out.fp_tbi - vcfeval_true_positive_baseline_vcf = RTGTOOLS_VCFEVAL.out.baseline_vcf - vcfeval_true_positive_baseline_vcf_tbi = RTGTOOLS_VCFEVAL.out.baseline_tbi - vcfeval_summary = RTGTOOLS_VCFEVAL.out.summary - vcfeval_phasing = RTGTOOLS_VCFEVAL.out.phasing - vcfeval_snp_roc = RTGTOOLS_VCFEVAL.out.snp_roc - vcfeval_non_snp_roc = RTGTOOLS_VCFEVAL.out.non_snp_roc - vcfeval_weighted_roc = RTGTOOLS_VCFEVAL.out.weighted_roc - - RTGTOOLS_ROCPLOT( - ch_rocplot_input - ) - - ch_versions = ch_versions.mix(RTGTOOLS_ROCPLOT.out.versions.first()) - - rocplot_out_png = RTGTOOLS_ROCPLOT.out.png - .branch { meta, png -> - roc_type = meta.roc_type - def new_meta = meta - meta.subMap("roc_type") - snp: roc_type == "snp" - non_snp: roc_type == "non_snp" - weighted: roc_type == "weighted" - } - - rocplot_out_svg = RTGTOOLS_ROCPLOT.out.svg - .branch { meta, svg -> - roc_type = meta.roc_type - def new_meta = meta - meta.subMap("roc_type") - - snp: roc_type == "snp" - non_snp: roc_type == "non_snp" - weighted: roc_type == "weighted" - } - - rtgtools_snp_png_rocplot = rocplot_out_png.snp - rtgtools_non_snp_png_rocplot = rocplot_out_png.non_snp - rtgtools_weighted_png_rocplot = rocplot_out_png.weighted - - rtgtools_snp_svg_rocplot = rocplot_out_svg.snp - rtgtools_non_snp_svg_rocplot = rocplot_out_svg.non_snp - rtgtools_weighted_svg_rocplot = rocplot_out_svg.weighted - } + vcfeval_true_positive_vcf = RTGTOOLS_VCFEVAL.out.tp_vcf + vcfeval_true_positive_vcf_tbi = RTGTOOLS_VCFEVAL.out.tp_tbi + vcfeval_false_negative_vcf = RTGTOOLS_VCFEVAL.out.fn_vcf + vcfeval_false_negative_vcf_tbi = RTGTOOLS_VCFEVAL.out.fn_tbi + vcfeval_false_positive_vcf = RTGTOOLS_VCFEVAL.out.fp_vcf + vcfeval_false_positive_vcf_tbi = RTGTOOLS_VCFEVAL.out.fp_tbi + vcfeval_true_positive_baseline_vcf = RTGTOOLS_VCFEVAL.out.baseline_vcf + vcfeval_true_positive_baseline_vcf_tbi = RTGTOOLS_VCFEVAL.out.baseline_tbi + vcfeval_summary = RTGTOOLS_VCFEVAL.out.summary + vcfeval_phasing = RTGTOOLS_VCFEVAL.out.phasing + vcfeval_snp_roc = RTGTOOLS_VCFEVAL.out.snp_roc + vcfeval_non_snp_roc = RTGTOOLS_VCFEVAL.out.non_snp_roc + vcfeval_weighted_roc = RTGTOOLS_VCFEVAL.out.weighted_roc + + RTGTOOLS_ROCPLOT( + ch_rocplot_input + ) + + ch_versions = ch_versions.mix(RTGTOOLS_ROCPLOT.out.versions.first()) + + rocplot_out_png = RTGTOOLS_ROCPLOT.out.png + .branch { meta, png -> + roc_type = meta.roc_type + def new_meta = meta - meta.subMap("roc_type") + + snp: roc_type == "snp" + non_snp: roc_type == "non_snp" + weighted: roc_type == "weighted" + } + + rocplot_out_svg = RTGTOOLS_ROCPLOT.out.svg + .branch { meta, svg -> + roc_type = meta.roc_type + def new_meta = meta - meta.subMap("roc_type") + + snp: roc_type == "snp" + non_snp: roc_type == "non_snp" + weighted: roc_type == "weighted" + } + + rtgtools_snp_png_rocplot = rocplot_out_png.snp + rtgtools_non_snp_png_rocplot = rocplot_out_png.non_snp + rtgtools_weighted_png_rocplot = rocplot_out_png.weighted + + rtgtools_snp_svg_rocplot = rocplot_out_svg.snp + rtgtools_non_snp_svg_rocplot = rocplot_out_svg.non_snp + rtgtools_weighted_svg_rocplot = rocplot_out_svg.weighted emit: - happy_vcf // channel: [ meta, vcf ] - happy_tbi // channel: [ meta, tbi ] - happy_indel_roc // channel: [ meta, csv ] - happy_indel_roc_pass // channel: [ meta, csv ] - happy_snp_roc // channel: [ meta, csv ] - happy_snp_roc_pass // channel: [ meta, csv ] - happy_roc // channel: [ meta, csv ] - happy_summary // channel: [ meta, csv ] - happy_extended_csv // channel: [ meta, csv ] - vcfeval_true_positive_vcf // channel: [ meta, vcf ] vcfeval_true_positive_vcf_tbi // channel: [ meta, tbi ] vcfeval_false_negative_vcf // channel: [ meta, vcf ] diff --git a/tests/pipeline/callers/main.nf.test.snap b/tests/pipeline/callers/main.nf.test.snap index b6f693f0..babe4775 100644 --- a/tests/pipeline/callers/main.nf.test.snap +++ b/tests/pipeline/callers/main.nf.test.snap @@ -2,23 +2,26 @@ "haplotypecaller": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -29,37 +32,41 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:40:41.593827142" + "timestamp": "2024-09-05T11:39:15.537730988" }, "vardict + haplotypecaller": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -70,15 +77,19 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/NA24143.vardict.ped", "test/Ashkenazim/NA24143.vardict.vcf.gz", + "test/Ashkenazim/NA24143.vardict.vcf.gz.csi", "test/Ashkenazim/NA24143.vardict.vcf.gz.tbi", "test/Ashkenazim/NA24149.vardict.ped", "test/Ashkenazim/NA24149.vardict.vcf.gz", + "test/Ashkenazim/NA24149.vardict.vcf.gz.csi", "test/Ashkenazim/NA24149.vardict.vcf.gz.tbi", "test/Ashkenazim/NA24385.vardict.ped", "test/Ashkenazim/NA24385.vardict.vcf.gz", + "test/Ashkenazim/NA24385.vardict.vcf.gz.csi", "test/Ashkenazim/NA24385.vardict.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html", @@ -91,15 +102,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:41:56.768447097" + "timestamp": "2024-09-05T11:56:32.019963111" }, "vardict": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", @@ -116,12 +127,15 @@ "samplesheet.csv", "test/Ashkenazim/NA24143.vardict.ped", "test/Ashkenazim/NA24143.vardict.vcf.gz", + "test/Ashkenazim/NA24143.vardict.vcf.gz.csi", "test/Ashkenazim/NA24143.vardict.vcf.gz.tbi", "test/Ashkenazim/NA24149.vardict.ped", "test/Ashkenazim/NA24149.vardict.vcf.gz", + "test/Ashkenazim/NA24149.vardict.vcf.gz.csi", "test/Ashkenazim/NA24149.vardict.vcf.gz.tbi", "test/Ashkenazim/NA24385.vardict.ped", "test/Ashkenazim/NA24385.vardict.vcf.gz", + "test/Ashkenazim/NA24385.vardict.vcf.gz.csi", "test/Ashkenazim/NA24385.vardict.vcf.gz.tbi", "test/Ashkenazim/reports/NA24143.vardict.bcftools_stats.txt", "test/Ashkenazim/reports/NA24143.vardict.somalier.html", @@ -132,9 +146,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:39:37.704366119" + "timestamp": "2024-09-05T11:54:10.944847435" } } \ No newline at end of file diff --git a/tests/pipeline/default/main.nf.test.snap b/tests/pipeline/default/main.nf.test.snap index 4e35a9bf..30d78cd0 100644 --- a/tests/pipeline/default/main.nf.test.snap +++ b/tests/pipeline/default/main.nf.test.snap @@ -2,23 +2,26 @@ "default": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -29,15 +32,16 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:34:28.414261433" + "timestamp": "2024-09-05T11:40:36.127517277" } } \ No newline at end of file diff --git a/tests/pipeline/gvcfs/main.nf.test.snap b/tests/pipeline/gvcfs/main.nf.test.snap index 430c3e0a..03a3b401 100644 --- a/tests/pipeline/gvcfs/main.nf.test.snap +++ b/tests/pipeline/gvcfs/main.nf.test.snap @@ -2,7 +2,7 @@ "gvcfs": { "content": [ [ - + "[:]" ], [ "multiqc/multiqc_plots", @@ -11,15 +11,16 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T17:18:10.515388658" + "timestamp": "2024-09-05T11:41:32.108980116" } } \ No newline at end of file diff --git a/tests/pipeline/variations/main.nf.test.snap b/tests/pipeline/variations/main.nf.test.snap index 988e32fc..ee31f079 100644 --- a/tests/pipeline/variations/main.nf.test.snap +++ b/tests/pipeline/variations/main.nf.test.snap @@ -2,23 +2,26 @@ "filter": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -29,37 +32,41 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:57:27.216291382" + "timestamp": "2024-09-05T11:45:02.491962487" }, "only_call": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -70,31 +77,34 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:58:10.801784853" + "timestamp": "2024-09-05T11:45:47.266012698" }, "annotate + vcfanno": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -105,37 +115,42 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.gzi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:56:25.391105365" + "timestamp": "2024-09-05T11:43:47.539727235" }, "automap": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -146,6 +161,7 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/automap_haplotypecaller/sample1/sample1.HomRegions.cmgg_bio.tsv", "test/Ashkenazim/automap_haplotypecaller/sample1/sample1.HomRegions.pdf", @@ -164,31 +180,34 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-04-04T16:27:21.116595696" + "timestamp": "2024-09-05T11:47:48.972236882" }, "only_merge": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -200,31 +219,34 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T16:28:12.406463008" + "timestamp": "2024-09-05T11:46:37.403799074" }, "annotate": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -235,15 +257,16 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T15:47:35.270453118" + "timestamp": "2024-09-05T11:42:39.793880467" } } \ No newline at end of file diff --git a/tests/pipeline/variations2/main.nf.test.snap b/tests/pipeline/variations2/main.nf.test.snap index af8cfcfd..ba145d7e 100644 --- a/tests/pipeline/variations2/main.nf.test.snap +++ b/tests/pipeline/variations2/main.nf.test.snap @@ -2,23 +2,26 @@ "gemini": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -30,37 +33,41 @@ "test/Ashkenazim/Ashkenazim.haplotypecaller.db", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T16:31:52.936259443" + "timestamp": "2024-09-05T11:59:55.764681555" }, "normalize": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -71,37 +78,41 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T17:04:19.112262269" + "timestamp": "2024-09-05T11:57:36.725019238" }, "updio": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -112,37 +123,41 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T16:30:38.464359399" + "timestamp": "2024-09-05T11:58:51.377552309" }, "add_ped": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", "NA24143/reports/NA24143.summary.txt", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", "NA24149/reports/NA24149.summary.txt", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -153,25 +168,27 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T17:09:21.531982672" + "timestamp": "2024-09-05T12:02:31.850254513" }, "validate": { "content": [ [ - + "[:]" ], [ "NA24143/NA24143.bed", "NA24143/NA24143.haplotypecaller.g.vcf.gz", + "NA24143/NA24143.haplotypecaller.g.vcf.gz.csi", "NA24143/NA24143.haplotypecaller.g.vcf.gz.tbi", "NA24143/reports/NA24143.global.dist.txt", "NA24143/reports/NA24143.haplotypecaller.bcftools_stats.txt", @@ -197,6 +214,7 @@ "NA24143/validation/haplotypecaller/NA24143.weighted_roc.tsv.gz", "NA24149/NA24149.bed", "NA24149/NA24149.haplotypecaller.g.vcf.gz", + "NA24149/NA24149.haplotypecaller.g.vcf.gz.csi", "NA24149/NA24149.haplotypecaller.g.vcf.gz.tbi", "NA24149/reports/NA24149.global.dist.txt", "NA24149/reports/NA24149.haplotypecaller.bcftools_stats.txt", @@ -222,6 +240,7 @@ "NA24149/validation/haplotypecaller/NA24149.weighted_roc.tsv.gz", "NA24385/NA24385.bed", "NA24385/NA24385.haplotypecaller.g.vcf.gz", + "NA24385/NA24385.haplotypecaller.g.vcf.gz.csi", "NA24385/NA24385.haplotypecaller.g.vcf.gz.tbi", "NA24385/reports/NA24385.global.dist.txt", "NA24385/reports/NA24385.haplotypecaller.bcftools_stats.txt", @@ -251,15 +270,16 @@ "test/Ashkenazim/Ashkenazim.bed", "test/Ashkenazim/Ashkenazim.haplotypecaller.ped", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz", + "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.csi", "test/Ashkenazim/Ashkenazim.haplotypecaller.vcf.gz.tbi", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.bcftools_stats.txt", "test/Ashkenazim/reports/Ashkenazim.haplotypecaller.somalier.html" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T16:33:15.226868795" + "timestamp": "2024-09-05T12:01:21.850991249" } } \ No newline at end of file diff --git a/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test b/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test index 7ad15931..33425c77 100644 --- a/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test +++ b/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test @@ -53,8 +53,8 @@ nextflow_workflow { [id:"strtablefile"], file(params.strtablefile, checkIfExists:true) ]) - input[6] = [] - input[7] = [] + input[6] = [[],[]] + input[7] = [[],[]] input[8] = false input[9] = false input[10] = false @@ -106,10 +106,8 @@ nextflow_workflow { [id:"strtablefile"], file(params.strtablefile, checkIfExists:true) ]) - input[6] = [] - input[7] = [] - input[6] = [] - input[7] = [] + input[6] = [[],[]] + input[7] = [[],[]] input[8] = false input[9] = false input[10] = false @@ -180,10 +178,8 @@ nextflow_workflow { [id:"strtablefile"], file(params.strtablefile, checkIfExists:true) ]) - input[6] = [] - input[7] = [] - input[6] = [] - input[7] = [] + input[6] = [[],[]] + input[7] = [[],[]] input[8] = false input[9] = false input[10] = false @@ -255,10 +251,8 @@ nextflow_workflow { [id:"strtablefile"], file(params.strtablefile, checkIfExists:true) ]) - input[6] = [] - input[7] = [] - input[6] = [] - input[7] = [] + input[6] = [[],[]] + input[7] = [[],[]] input[8] = false input[9] = false input[10] = false @@ -330,10 +324,8 @@ nextflow_workflow { [id:"strtablefile"], file(params.strtablefile, checkIfExists:true) ]) - input[6] = [] - input[7] = [] - input[6] = [] - input[7] = [] + input[6] = [[],[]] + input[7] = [[],[]] input[8] = false input[9] = true input[10] = false @@ -405,10 +397,8 @@ nextflow_workflow { [id:"strtablefile"], file(params.strtablefile, checkIfExists:true) ]) - input[6] = [] - input[7] = [] - input[6] = [] - input[7] = [] + input[6] = [[],[]] + input[7] = [[],[]] input[8] = false input[9] = false input[10] = true @@ -479,10 +469,8 @@ nextflow_workflow { [id:"strtablefile"], file(params.strtablefile, checkIfExists:true) ]) - input[6] = [] - input[7] = [] - input[6] = [] - input[7] = [] + input[6] = [[],[]] + input[7] = [[],[]] input[8] = false input[9] = false input[10] = false diff --git a/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap b/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap index 64e23b12..6c932f93 100644 --- a/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap +++ b/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap @@ -6,15 +6,15 @@ ], [ [ - "NA24835.haplotypecaller.bcftools_stats.txt:md5,cf8d900f4a7f7844bf1ece4478010459" + "NA24835.haplotypecaller.bcftools_stats.txt:md5,5f42bee02b2bd0d2af2954292ec3b422" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T10:12:27.678293492" + "timestamp": "2024-09-05T11:20:45.005084818" }, "default - family": { "content": [ @@ -33,15 +33,15 @@ ], [ [ - "NA24835.haplotypecaller.bcftools_stats.txt:md5,cf8d900f4a7f7844bf1ece4478010459" + "NA24835.haplotypecaller.bcftools_stats.txt:md5,5f42bee02b2bd0d2af2954292ec3b422" ] ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-06T13:01:36.711373912" + "timestamp": "2024-09-05T11:18:02.353352239" }, "filter - family": { "content": [ @@ -60,15 +60,15 @@ ], [ [ - "NA24835.haplotypecaller.bcftools_stats.txt:md5,cf8d900f4a7f7844bf1ece4478010459" + "NA24835.haplotypecaller.bcftools_stats.txt:md5,5f42bee02b2bd0d2af2954292ec3b422" ] ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-06T13:02:26.651064532" + "timestamp": "2024-09-05T11:19:14.883570897" }, "default - gvcfs": { "content": [ @@ -112,15 +112,15 @@ ], [ [ - "NA24143.haplotypecaller.bcftools_stats.txt:md5,8832acfa6af30e9225b151da201733c3" + "NA24143.haplotypecaller.bcftools_stats.txt:md5,09b4e7674e0f5b98b1e548df3002250e" ] ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-06T12:55:51.608812907" + "timestamp": "2024-09-05T11:16:25.448441115" }, "only_call - family": { "content": [ @@ -129,15 +129,15 @@ ], [ [ - "NA24835.haplotypecaller.bcftools_stats.txt:md5,cf8d900f4a7f7844bf1ece4478010459" + "NA24835.haplotypecaller.bcftools_stats.txt:md5,5f42bee02b2bd0d2af2954292ec3b422" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T10:11:35.142110509" + "timestamp": "2024-09-05T11:20:04.714403906" }, "only_merge - sample + family": { "content": [ @@ -156,14 +156,14 @@ ], [ [ - "NA24835.haplotypecaller.bcftools_stats.txt:md5,cf8d900f4a7f7844bf1ece4478010459" + "NA24835.haplotypecaller.bcftools_stats.txt:md5,5f42bee02b2bd0d2af2954292ec3b422" ] ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-06T13:04:20.473178165" + "timestamp": "2024-09-05T11:21:57.601081087" } } \ No newline at end of file diff --git a/tests/subworkflows/local/cram_call_vardictjava/main.nf.test b/tests/subworkflows/local/cram_call_vardictjava/main.nf.test index 6cf959b0..b0914d97 100644 --- a/tests/subworkflows/local/cram_call_vardictjava/main.nf.test +++ b/tests/subworkflows/local/cram_call_vardictjava/main.nf.test @@ -48,8 +48,8 @@ nextflow_workflow { [id:"fai"], file(params.fai, checkIfExists:true) ]) - input[4] = [] - input[5] = [] + input[4] = [[],[]] + input[5] = [[],[]] input[6] = false """ } @@ -105,8 +105,8 @@ nextflow_workflow { [id:"fai"], file(params.fai, checkIfExists:true) ]) - input[4] = [] - input[5] = [] + input[4] = [[],[]] + input[5] = [[],[]] input[6] = true """ } @@ -180,8 +180,8 @@ nextflow_workflow { [id:"fai"], file(params.fai, checkIfExists:true) ]) - input[4] = [] - input[5] = [] + input[4] = [[],[]] + input[5] = [[],[]] input[6] = false """ } diff --git a/tests/subworkflows/local/vcf_annotation/main.nf.test.snap b/tests/subworkflows/local/vcf_annotation/main.nf.test.snap index fdec0b82..12d0ef2c 100644 --- a/tests/subworkflows/local/vcf_annotation/main.nf.test.snap +++ b/tests/subworkflows/local/vcf_annotation/main.nf.test.snap @@ -13,16 +13,16 @@ ] ], [ - "NA241431_annotated.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", - "NA241432_annotated.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", - "NA241433_annotated.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + "NA241430_annotated_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "NA241431_annotated_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "NA241432_annotated_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-28T09:26:20.34701886" + "timestamp": "2024-09-05T12:53:05.739638954" }, "vcfanno": { "content": [ @@ -38,15 +38,15 @@ ] ], [ - "NA241431_annotated.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", - "NA241432_annotated.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", - "NA241433_annotated.summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + "NA241430_annotated_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "NA241431_annotated_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "NA241432_annotated_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-28T09:26:37.223392102" + "timestamp": "2024-09-05T12:53:27.894947052" } } \ No newline at end of file diff --git a/tests/subworkflows/local/vcf_extract_relate_somalier/main.nf.test b/tests/subworkflows/local/vcf_extract_relate_somalier/main.nf.test index 09aa4cca..a07570e9 100644 --- a/tests/subworkflows/local/vcf_extract_relate_somalier/main.nf.test +++ b/tests/subworkflows/local/vcf_extract_relate_somalier/main.nf.test @@ -18,9 +18,9 @@ nextflow_workflow { file(params.famvcf, checkIfExists:true), file(params.famtbi, checkIfExists:true) ]) - input[1] = Channel.value(file(params.fasta, checkIfExists:true)) - input[2] = Channel.value(file(params.fai, checkIfExists:true)) - input[3] = Channel.value(file(params.somalier_sites, checkIfExists:true)) + input[1] = Channel.value([[id:"ref"], file(params.fasta, checkIfExists:true)]) + input[2] = Channel.value([[id:"ref"], file(params.fai, checkIfExists:true)]) + input[3] = Channel.value([[id:"ref"], file(params.somalier_sites, checkIfExists:true)]) input[4] = Channel.of([ [id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller"], file(params.ped, checkIfExists:true) @@ -54,9 +54,9 @@ nextflow_workflow { file(params.famvcf, checkIfExists:true), file(params.famtbi, checkIfExists:true) ]) - input[1] = Channel.value(file(params.fasta, checkIfExists:true)) - input[2] = Channel.value(file(params.fai, checkIfExists:true)) - input[3] = Channel.value(file(params.somalier_sites, checkIfExists:true)) + input[1] = Channel.value([[id:"ref"], file(params.fasta, checkIfExists:true)]) + input[2] = Channel.value([[id:"ref"], file(params.fai, checkIfExists:true)]) + input[3] = Channel.value([[id:"ref"], file(params.somalier_sites, checkIfExists:true)]) input[4] = Channel.of([ [id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller"], [] diff --git a/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test b/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test index b77bd568..f540a89c 100644 --- a/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test +++ b/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test @@ -45,10 +45,6 @@ nextflow_workflow { input[2] = [[],[]] input[3] = [[],[]] input[4] = UNTAR.out.untar - input[5] = [[],[]] - input[6] = [[],[]] - input[7] = [[],[]] - input[8] = "vcfeval" """ } } @@ -57,15 +53,6 @@ nextflow_workflow { assertAll( { assert workflow.success }, { assert snapshot( - workflow.out.happy_vcf, - workflow.out.happy_tbi, - workflow.out.happy_indel_roc, - workflow.out.happy_indel_roc_pass, - workflow.out.happy_snp_roc, - workflow.out.happy_snp_roc_pass, - workflow.out.happy_roc, - workflow.out.happy_summary, - workflow.out.happy_extended_csv, workflow.out.vcfeval_true_positive_vcf, workflow.out.vcfeval_true_positive_vcf_tbi, workflow.out.vcfeval_false_negative_vcf, diff --git a/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test.snap b/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test.snap index 8639b840..3e0b9a14 100644 --- a/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test.snap +++ b/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test.snap @@ -1,33 +1,6 @@ { "default": { "content": [ - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], [ [ { @@ -245,9 +218,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T14:02:50.290466115" + "timestamp": "2024-09-04T17:19:41.712263383" } } \ No newline at end of file diff --git a/workflows/germline.nf b/workflows/germline.nf index 6fe460dc..a756f7aa 100644 --- a/workflows/germline.nf +++ b/workflows/germline.nf @@ -136,17 +136,17 @@ workflow GERMLINE { // ch_fasta_ready = Channel.fromPath(fasta).map{ fasta_file -> [[id:"reference"], fasta_file] }.collect() - ch_fai = fai ? Channel.fromPath(fai).map{ fai_file -> [[id:"reference"], fai_file] }.collect() : null - ch_dict = dict ? Channel.fromPath(dict).map{ dict_file -> [[id:"reference"], dict_file] }.collect() : null - ch_strtablefile = strtablefile ? Channel.fromPath(strtablefile).map{ str_file -> [[id:"reference"], str_file] }.collect() : null - ch_sdf = sdf ? Channel.fromPath(sdf).map { sdf_file -> [[id:'reference'], sdf_file] }.collect() : null + ch_fai = fai ? Channel.fromPath(fai).map{ fai_file -> [[id:"reference"], fai_file] }.collect() : null + ch_dict = dict ? Channel.fromPath(dict).map{ dict_file -> [[id:"reference"], dict_file] }.collect() : null + ch_strtablefile = strtablefile ? Channel.fromPath(strtablefile).map{ str_file -> [[id:"reference"], str_file] }.collect() : null + ch_sdf = sdf ? Channel.fromPath(sdf).map { sdf_file -> [[id:'reference'], sdf_file] }.collect() : null ch_default_roi = roi ? Channel.fromPath(roi).collect() : [] - ch_dbsnp_ready = dbsnp ? Channel.fromPath(dbsnp).collect() : [] - ch_dbsnp_tbi = dbsnp_tbi ? Channel.fromPath(dbsnp_tbi).collect() : [] + ch_dbsnp_ready = dbsnp ? Channel.fromPath(dbsnp).collect { dbsnp_file -> [[id:"dbsnp"], dbsnp_file] } : [[],[]] + ch_dbsnp_tbi = dbsnp_tbi ? Channel.fromPath(dbsnp_tbi).collect { dbsnp_file -> [[id:"dbsnp"], dbsnp_file] } : [[],[]] - ch_somalier_sites = somalier_sites ? Channel.fromPath(somalier_sites).collect() : [] + ch_somalier_sites = somalier_sites ? Channel.fromPath(somalier_sites).collect { sites_file -> [[id:"somalier_sites"], sites_file] } : [[],[]] ch_vep_cache = vep_cache ? Channel.fromPath(vep_cache).collect() : [] @@ -518,8 +518,8 @@ workflow GERMLINE { VCF_EXTRACT_RELATE_SOMALIER( ch_normalized_variants, - ch_fasta_ready.map { meta, fasta_file -> fasta_file }, - ch_fai_ready.map { meta, fai_file -> fai_file }, + ch_fasta_ready, + ch_fai_ready, ch_somalier_sites, ch_somalier_input ) @@ -672,11 +672,7 @@ workflow GERMLINE { ch_validation_input.bed, ch_fasta_ready, ch_fai_ready, - ch_sdf_ready.collect(), - [[],[]], - [[],[]], - [[],[]], - "vcfeval" //Only VCFeval for now, awaiting the conda fix for happy (https://github.com/bioconda/bioconda-recipes/pull/39267) + ch_sdf_ready.collect() ) ch_versions = ch_versions.mix(VCF_VALIDATE_SMALL_VARIANTS.out.versions) } From 0a9c6b83f7276d3a4cbed242b15baf5a57c3b2ea Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 10 Sep 2024 13:47:04 +0200 Subject: [PATCH 31/49] nf-core modules update (#193) --- modules.json | 82 +++++------ .../bcftools/annotate/bcftools-annotate.diff | 12 +- .../nf-core/bcftools/annotate/environment.yml | 2 - .../nf-core/bcftools/concat/environment.yml | 2 - .../nf-core/bcftools/filter/environment.yml | 2 - modules/nf-core/bcftools/norm/environment.yml | 2 - .../bcftools/pluginscatter/environment.yml | 2 - .../nf-core/bcftools/query/environment.yml | 2 - .../nf-core/bcftools/reheader/environment.yml | 2 - modules/nf-core/bcftools/sort/environment.yml | 2 - .../nf-core/bcftools/stats/environment.yml | 2 - .../bedtools/intersect/environment.yml | 2 - .../nf-core/bedtools/merge/environment.yml | 2 - .../nf-core/bedtools/merge/tests/main.nf.test | 34 +++++ .../bedtools/merge/tests/main.nf.test.snap | 35 +++++ .../bedtools/merge/tests/nextflow.config | 7 + modules/nf-core/bedtools/merge/tests/tags.yml | 2 + .../nf-core/bedtools/split/environment.yml | 2 - .../nf-core/bedtools/split/tests/main.nf.test | 36 +++++ .../bedtools/split/tests/main.nf.test.snap | 41 ++++++ .../ensemblvep/download/environment.yml | 2 - .../nf-core/ensemblvep/vep/environment.yml | 2 - .../calibratedragstrmodel/environment.yml | 2 - .../calibratedragstrmodel/tests/main.nf.test | 137 ++++++++++++++++++ .../tests/main.nf.test.snap | 78 ++++++++++ .../gatk4/composestrtablefile/environment.yml | 2 - .../composestrtablefile/tests/main.nf.test | 38 +++++ .../tests/main.nf.test.snap | 15 ++ .../createsequencedictionary/environment.yml | 2 - .../tests/main.nf.test | 56 +++++++ .../tests/main.nf.test.snap | 68 +++++++++ .../createsequencedictionary/tests/tags.yml | 2 + .../gatk4/genomicsdbimport/environment.yml | 2 - .../gatk4/genomicsdbimport/tests/main.nf.test | 41 +++--- .../genomicsdbimport/tests/main.nf.test.snap | 92 +++++++++--- .../gatk4/genotypegvcfs/environment.yml | 2 - .../gatk4/haplotypecaller/environment.yml | 2 - .../gatk4-haplotypecaller.diff | 30 ---- modules/nf-core/gatk4/haplotypecaller/main.nf | 2 +- modules/nf-core/gawk/environment.yml | 2 - modules/nf-core/mosdepth/environment.yml | 2 - modules/nf-core/multiqc/environment.yml | 2 - .../nf-core/rtgtools/format/environment.yml | 2 - modules/nf-core/rtgtools/format/meta.yml | 2 +- .../rtgtools/pedfilter/environment.yml | 2 - .../pedfilter/rtgtools-pedfilter.diff | 6 +- .../nf-core/rtgtools/rocplot/environment.yml | 2 - .../nf-core/rtgtools/vcfeval/environment.yml | 2 - modules/nf-core/rtgtools/vcfeval/meta.yml | 2 +- .../nf-core/samtools/convert/environment.yml | 2 - .../nf-core/samtools/faidx/environment.yml | 3 - .../nf-core/samtools/index/environment.yml | 2 - .../nf-core/samtools/merge/environment.yml | 2 - modules/nf-core/snpeff/snpeff/environment.yml | 2 - .../nf-core/somalier/extract/environment.yml | 2 - .../nf-core/somalier/relate/environment.yml | 2 - .../somalier/relate/somalier-relate.diff | 6 +- modules/nf-core/tabix/bgzip/environment.yml | 2 - .../nf-core/tabix/bgziptabix/environment.yml | 2 - modules/nf-core/tabix/tabix/environment.yml | 3 - modules/nf-core/untar/environment.yml | 2 - modules/nf-core/vardictjava/environment.yml | 2 - modules/nf-core/vcf2db/environment.yml | 2 - modules/nf-core/vcfanno/environment.yml | 2 - modules/nf-core/vcfanno/tests/main.nf.test | 22 +-- 65 files changed, 714 insertions(+), 216 deletions(-) create mode 100644 modules/nf-core/bedtools/merge/tests/main.nf.test create mode 100644 modules/nf-core/bedtools/merge/tests/main.nf.test.snap create mode 100644 modules/nf-core/bedtools/merge/tests/nextflow.config create mode 100644 modules/nf-core/bedtools/merge/tests/tags.yml create mode 100644 modules/nf-core/bedtools/split/tests/main.nf.test create mode 100644 modules/nf-core/bedtools/split/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/createsequencedictionary/tests/tags.yml delete mode 100644 modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff diff --git a/modules.json b/modules.json index b9a65237..9693296c 100644 --- a/modules.json +++ b/modules.json @@ -7,210 +7,210 @@ "nf-core": { "bcftools/annotate": { "branch": "master", - "git_sha": "88ae68490e8f2478a1e1bbeedac970fd7cc73022", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"], "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff" }, "bcftools/concat": { "branch": "master", - "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/filter": { "branch": "master", - "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "bcftools/norm": { "branch": "master", - "git_sha": "f6cc00f107826cfaf1c933297b10ed1757b41479", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "bcftools/pluginscatter": { "branch": "master", - "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/query": { "branch": "master", - "git_sha": "34ac993e081b32d2170ab790d0386b74122f9d36", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", - "git_sha": "c32611ac6813055b9321d2827678e2f8aebcb394", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", - "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/stats": { "branch": "master", - "git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "bedtools/intersect": { "branch": "master", - "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "bedtools/merge": { "branch": "master", - "git_sha": "a3d614e4a7b8691a259bcfe33ad80903217d6215", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "bedtools/split": { "branch": "master", - "git_sha": "6dc8a32e32158bb4d3f9af92c802233b5d4f8e4d", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "ensemblvep/download": { "branch": "master", - "git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", - "git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "gatk4/calibratedragstrmodel": { "branch": "master", - "git_sha": "3f42e07a1133064c569b0dbe182979527bca9e59", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "gatk4/composestrtablefile": { "branch": "master", - "git_sha": "926e2f394d01c71d3abbdbca9c588630bfe51abf", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", - "git_sha": "e6fe277739f5894711405af3e717b2470bd956b5", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "gatk4/genomicsdbimport": { "branch": "master", - "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "gatk4/genotypegvcfs": { "branch": "master", - "git_sha": "8b74c800af3d91e0d7bfbecb902308dc4369071c", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "gatk4/haplotypecaller": { "branch": "master", - "git_sha": "c332ea831f95f750be962c4b5de655f7a1e6e245", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "gawk": { "branch": "master", - "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "mosdepth": { "branch": "master", - "git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "19ca321db5d8bd48923262c2eca6422359633491", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "rtgtools/format": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", "installed_by": ["modules"] }, "rtgtools/pedfilter": { "branch": "master", - "git_sha": "c1c2a770cfb0bfbf093a2434a27f091ebbc65987", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"], "patch": "modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff" }, "rtgtools/rocplot": { "branch": "master", - "git_sha": "64770369d851c45c364e410e052ef9a6c3a7d2bb", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "rtgtools/vcfeval": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", "installed_by": ["modules"] }, "samtools/convert": { "branch": "master", - "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", - "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "samtools/index": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", - "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "snpeff/snpeff": { "branch": "master", - "git_sha": "3ad7292d9b8da881386e9d5b58364d7da489b38b", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "somalier/extract": { "branch": "master", - "git_sha": "458c882987320e27fc90723ec96c127a243a5497", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "somalier/relate": { "branch": "master", - "git_sha": "458c882987320e27fc90723ec96c127a243a5497", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"], "patch": "modules/nf-core/somalier/relate/somalier-relate.diff" }, "tabix/bgzip": { "branch": "master", - "git_sha": "b20be35facfc5acdc1259f132ed79339d79e989f", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", - "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "tabix/tabix": { "branch": "master", - "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff"] }, "untar": { "branch": "master", - "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "vardictjava": { "branch": "master", - "git_sha": "e61e5a13ef49c5595986bd31efb85c3f0709a282", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "vcf2db": { "branch": "master", - "git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] }, "vcfanno": { "branch": "master", - "git_sha": "9a8bba5910982ae637dedb8664e3121db77e173f", + "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", "installed_by": ["modules"] } } diff --git a/modules/nf-core/bcftools/annotate/bcftools-annotate.diff b/modules/nf-core/bcftools/annotate/bcftools-annotate.diff index 518cee56..ae2c685f 100644 --- a/modules/nf-core/bcftools/annotate/bcftools-annotate.diff +++ b/modules/nf-core/bcftools/annotate/bcftools-annotate.diff @@ -1,4 +1,6 @@ Changes in module 'nf-core/bcftools/annotate' +'modules/nf-core/bcftools/annotate/environment.yml' is unchanged +'modules/nf-core/bcftools/annotate/meta.yml' is unchanged Changes in 'bcftools/annotate/main.nf': --- modules/nf-core/bcftools/annotate/main.nf +++ modules/nf-core/bcftools/annotate/main.nf @@ -13,14 +15,12 @@ Changes in 'bcftools/annotate/main.nf': output: tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf -'modules/nf-core/bcftools/annotate/environment.yml' is unchanged -'modules/nf-core/bcftools/annotate/meta.yml' is unchanged +'modules/nf-core/bcftools/annotate/tests/main.nf.test.snap' is unchanged 'modules/nf-core/bcftools/annotate/tests/tags.yml' is unchanged -'modules/nf-core/bcftools/annotate/tests/vcf.config' is unchanged -'modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config' is unchanged +'modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config' is unchanged 'modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config' is unchanged +'modules/nf-core/bcftools/annotate/tests/vcf.config' is unchanged 'modules/nf-core/bcftools/annotate/tests/main.nf.test' is unchanged 'modules/nf-core/bcftools/annotate/tests/bcf.config' is unchanged -'modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config' is unchanged -'modules/nf-core/bcftools/annotate/tests/main.nf.test.snap' is unchanged +'modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config' is unchanged ************************************************************ diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml index 3d4e3379..5c00b116 100644 --- a/modules/nf-core/bcftools/annotate/environment.yml +++ b/modules/nf-core/bcftools/annotate/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_annotate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml index 6544e949..5c00b116 100644 --- a/modules/nf-core/bcftools/concat/environment.yml +++ b/modules/nf-core/bcftools/concat/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_concat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/filter/environment.yml b/modules/nf-core/bcftools/filter/environment.yml index 854de139..5c00b116 100644 --- a/modules/nf-core/bcftools/filter/environment.yml +++ b/modules/nf-core/bcftools/filter/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_filter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/norm/environment.yml b/modules/nf-core/bcftools/norm/environment.yml index 0c7dfa8f..5c00b116 100644 --- a/modules/nf-core/bcftools/norm/environment.yml +++ b/modules/nf-core/bcftools/norm/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_norm channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/pluginscatter/environment.yml b/modules/nf-core/bcftools/pluginscatter/environment.yml index 51bce4d3..5c00b116 100644 --- a/modules/nf-core/bcftools/pluginscatter/environment.yml +++ b/modules/nf-core/bcftools/pluginscatter/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_pluginscatter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/query/environment.yml b/modules/nf-core/bcftools/query/environment.yml index d8c4f4e4..5c00b116 100644 --- a/modules/nf-core/bcftools/query/environment.yml +++ b/modules/nf-core/bcftools/query/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_query channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/reheader/environment.yml b/modules/nf-core/bcftools/reheader/environment.yml index 48fd72c9..5c00b116 100644 --- a/modules/nf-core/bcftools/reheader/environment.yml +++ b/modules/nf-core/bcftools/reheader/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_reheader channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml index 2295ecfd..5c00b116 100644 --- a/modules/nf-core/bcftools/sort/environment.yml +++ b/modules/nf-core/bcftools/sort/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_sort channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/stats/environment.yml b/modules/nf-core/bcftools/stats/environment.yml index 128fe204..93357b41 100644 --- a/modules/nf-core/bcftools/stats/environment.yml +++ b/modules/nf-core/bcftools/stats/environment.yml @@ -1,8 +1,6 @@ -name: bcftools_stats channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/bedtools/intersect/environment.yml b/modules/nf-core/bedtools/intersect/environment.yml index 2a343050..5683bc05 100644 --- a/modules/nf-core/bedtools/intersect/environment.yml +++ b/modules/nf-core/bedtools/intersect/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_intersect channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/merge/environment.yml b/modules/nf-core/bedtools/merge/environment.yml index 99707878..5683bc05 100644 --- a/modules/nf-core/bedtools/merge/environment.yml +++ b/modules/nf-core/bedtools/merge/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/merge/tests/main.nf.test b/modules/nf-core/bedtools/merge/tests/main.nf.test new file mode 100644 index 00000000..2959d6b9 --- /dev/null +++ b/modules/nf-core/bedtools/merge/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test Process BEDTOOLS_MERGE" + script "../main.nf" + config "./nextflow.config" + process "BEDTOOLS_MERGE" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/merge" + + test("test_bedtools_merge") { + + when { + process { + """ + input[0] = [ [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/merge/tests/main.nf.test.snap b/modules/nf-core/bedtools/merge/tests/main.nf.test.snap new file mode 100644 index 00000000..ee6c4e63 --- /dev/null +++ b/modules/nf-core/bedtools/merge/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "test_bedtools_merge": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_out.bed:md5,0cf6ed2b6f470cd44a247da74ca4fe4e" + ] + ], + "1": [ + "versions.yml:md5,2d134badb4cd1e4e903696c7967f28d6" + ], + "bed": [ + [ + { + "id": "test" + }, + "test_out.bed:md5,0cf6ed2b6f470cd44a247da74ca4fe4e" + ] + ], + "versions": [ + "versions.yml:md5,2d134badb4cd1e4e903696c7967f28d6" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T17:07:09.721153" + } +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/merge/tests/nextflow.config b/modules/nf-core/bedtools/merge/tests/nextflow.config new file mode 100644 index 00000000..16444e98 --- /dev/null +++ b/modules/nf-core/bedtools/merge/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: BEDTOOLS_MERGE { + ext.prefix = { "${meta.id}_out" } + } + +} diff --git a/modules/nf-core/bedtools/merge/tests/tags.yml b/modules/nf-core/bedtools/merge/tests/tags.yml new file mode 100644 index 00000000..60c8cad1 --- /dev/null +++ b/modules/nf-core/bedtools/merge/tests/tags.yml @@ -0,0 +1,2 @@ +bedtools/merge: + - "modules/nf-core/bedtools/merge/**" diff --git a/modules/nf-core/bedtools/split/environment.yml b/modules/nf-core/bedtools/split/environment.yml index 71912c7d..5683bc05 100644 --- a/modules/nf-core/bedtools/split/environment.yml +++ b/modules/nf-core/bedtools/split/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_split channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/split/tests/main.nf.test b/modules/nf-core/bedtools/split/tests/main.nf.test new file mode 100644 index 00000000..a59891b7 --- /dev/null +++ b/modules/nf-core/bedtools/split/tests/main.nf.test @@ -0,0 +1,36 @@ + +nextflow_process { + + name "Test Process BEDTOOLS_SPLIT" + script "../main.nf" + process "BEDTOOLS_SPLIT" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/split" + + test("test-bedtools-split") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true), + 2 + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bedtools/split/tests/main.nf.test.snap b/modules/nf-core/bedtools/split/tests/main.nf.test.snap new file mode 100644 index 00000000..359b3aa9 --- /dev/null +++ b/modules/nf-core/bedtools/split/tests/main.nf.test.snap @@ -0,0 +1,41 @@ +{ + "test-bedtools-split": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test.00001.bed:md5,d58e5e46c2fcc3b8be5db0f023e93cb5", + "test.00002.bed:md5,03caf952e9297a54620d2bbba8dc2823" + ] + ] + ], + "1": [ + "versions.yml:md5,33e0d5f886b7f0ed6f9c3e19b049357f" + ], + "beds": [ + [ + { + "id": "test" + }, + [ + "test.00001.bed:md5,d58e5e46c2fcc3b8be5db0f023e93cb5", + "test.00002.bed:md5,03caf952e9297a54620d2bbba8dc2823" + ] + ] + ], + "versions": [ + "versions.yml:md5,33e0d5f886b7f0ed6f9c3e19b049357f" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:50:28.137857" + } +} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml index 91564cce..283a45bb 100644 --- a/modules/nf-core/ensemblvep/download/environment.yml +++ b/modules/nf-core/ensemblvep/download/environment.yml @@ -1,7 +1,5 @@ -name: ensemblvep_download channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ensembl-vep=112.0 diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml index 3eae4fb1..283a45bb 100644 --- a/modules/nf-core/ensemblvep/vep/environment.yml +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -1,7 +1,5 @@ -name: ensemblvep_vep channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ensembl-vep=112.0 diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml index 810eade1..55993f44 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml +++ b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_calibratedragstrmodel channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test new file mode 100644 index 00000000..f06292f2 --- /dev/null +++ b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test @@ -0,0 +1,137 @@ + +nextflow_process { + + name "Test Process GATK4_CALIBRATEDRAGSTRMODEL" + script "../main.nf" + process "GATK4_CALIBRATEDRAGSTRMODEL" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/calibratedragstrmodel" + + test("test-gatk4-calibratedragstrmodel-bam") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_strtablefile.zip', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.dragstr_model[0][1]).readLines()[3..7], + process.out.versions + ).match() + } + ) + } + } + + test("test-gatk4-calibratedragstrmodel-cram") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_strtablefile.zip', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.dragstr_model[0][1]).readLines()[3..7], + process.out.versions + ).match() + } + ) + } + } + + test("test-gatk4-calibratedragstrmodel-beds") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_strtablefile.zip', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.dragstr_model[0][1]).readLines()[3..7], + process.out.versions + ).match() + } + ) + } + } + + test("test-gatk4-calibratedragstrmodel-gzipped-beds") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_strtablefile.zip', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.dragstr_model[0][1]).readLines()[3..7], + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap new file mode 100644 index 00000000..d0d7b8b9 --- /dev/null +++ b/modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap @@ -0,0 +1,78 @@ +{ + "test-gatk4-calibratedragstrmodel-bam": { + "content": [ + [ + "# sample = testN", + "# readGroups = 1", + "# estimatedOrDefaults = defaults", + "# commandLine = CalibrateDragstrModel --str-table-path genome_strtablefile.zip --threads 2 --output test.txt --input test.paired_end.sorted.bam --reference genome.fasta --tmp-dir . --gp-values 10:1.0:50 --api-values 0:1.0:40 --gop-values 10:.25:50 --het-to-hom-ratio 2.0 --min-loci-count 50 --api-mono-threshold 3 --max-period 8 --max-repeats 20 --minimum-depth 10 --pileup-padding 5 --sampling-min-mq 20 --parallel false --shard-size 1000000 --down-sample-size 4096 --force-estimation false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false", + "############################################################################################" + ], + [ + "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:22:17.584362" + }, + "test-gatk4-calibratedragstrmodel-cram": { + "content": [ + [ + "# sample = testN", + "# readGroups = 1", + "# estimatedOrDefaults = defaults", + "# commandLine = CalibrateDragstrModel --str-table-path genome_strtablefile.zip --threads 2 --output test.txt --input test.paired_end.sorted.cram --reference genome.fasta --tmp-dir . --gp-values 10:1.0:50 --api-values 0:1.0:40 --gop-values 10:.25:50 --het-to-hom-ratio 2.0 --min-loci-count 50 --api-mono-threshold 3 --max-period 8 --max-repeats 20 --minimum-depth 10 --pileup-padding 5 --sampling-min-mq 20 --parallel false --shard-size 1000000 --down-sample-size 4096 --force-estimation false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false", + "############################################################################################" + ], + [ + "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:22:30.21551" + }, + "test-gatk4-calibratedragstrmodel-gzipped-beds": { + "content": [ + [ + "# sample = testN", + "# readGroups = 1", + "# estimatedOrDefaults = defaults", + "# commandLine = CalibrateDragstrModel --str-table-path genome_strtablefile.zip --threads 2 --output test.txt --input test.paired_end.sorted.cram --reference genome.fasta --tmp-dir . --gp-values 10:1.0:50 --api-values 0:1.0:40 --gop-values 10:.25:50 --het-to-hom-ratio 2.0 --min-loci-count 50 --api-mono-threshold 3 --max-period 8 --max-repeats 20 --minimum-depth 10 --pileup-padding 5 --sampling-min-mq 20 --parallel false --shard-size 1000000 --down-sample-size 4096 --force-estimation false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false", + "############################################################################################" + ], + [ + "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:22:53.619871" + }, + "test-gatk4-calibratedragstrmodel-beds": { + "content": [ + [ + "# sample = testN", + "# readGroups = 1", + "# estimatedOrDefaults = defaults", + "# commandLine = CalibrateDragstrModel --str-table-path genome_strtablefile.zip --threads 2 --output test.txt --input test.paired_end.sorted.cram --reference genome.fasta --tmp-dir . --gp-values 10:1.0:50 --api-values 0:1.0:40 --gop-values 10:.25:50 --het-to-hom-ratio 2.0 --min-loci-count 50 --api-mono-threshold 3 --max-period 8 --max-repeats 20 --minimum-depth 10 --pileup-padding 5 --sampling-min-mq 20 --parallel false --shard-size 1000000 --down-sample-size 4096 --force-estimation false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false", + "############################################################################################" + ], + [ + "versions.yml:md5,3a652afb9cc9fca4e162ec205406b368" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:22:41.938548" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/composestrtablefile/environment.yml b/modules/nf-core/gatk4/composestrtablefile/environment.yml index ffbda0fb..55993f44 100644 --- a/modules/nf-core/gatk4/composestrtablefile/environment.yml +++ b/modules/nf-core/gatk4/composestrtablefile/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_composestrtablefile channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test new file mode 100644 index 00000000..7d066cf1 --- /dev/null +++ b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test @@ -0,0 +1,38 @@ + +nextflow_process { + + name "Test Process GATK4_COMPOSESTRTABLEFILE" + script "../main.nf" + process "GATK4_COMPOSESTRTABLEFILE" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/composestrtablefile" + + test("test-gatk4-composestrtablefile") { + + when { + process { + """ + input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.str_table[0]).name, + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap new file mode 100644 index 00000000..02136a8b --- /dev/null +++ b/modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap @@ -0,0 +1,15 @@ +{ + "test-gatk4-composestrtablefile": { + "content": [ + "genome.zip", + [ + "versions.yml:md5,755f9a44a99148151b624d70eb6ce260" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T13:37:10.366333" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml index 78822ad0..55993f44 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_createsequencedictionary channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test new file mode 100644 index 00000000..a8a9c6d2 --- /dev/null +++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test @@ -0,0 +1,56 @@ +nextflow_process { + + name "Test Process GATK4_CREATESEQUENCEDICTIONARY" + script "../main.nf" + process "GATK4_CREATESEQUENCEDICTIONARY" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/createsequencedictionary" + + test("sarscov2 - fasta") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - fasta - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap new file mode 100644 index 00000000..16735f95 --- /dev/null +++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "sarscov2 - fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "genome.dict:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + ], + "dict": [ + [ + { + "id": "test" + }, + "genome.dict:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-05-16T10:16:16.34453" + }, + "sarscov2 - fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "genome.dict:md5,7362679f176e0f52add03c08f457f646" + ] + ], + "1": [ + "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + ], + "dict": [ + [ + { + "id": "test" + }, + "genome.dict:md5,7362679f176e0f52add03c08f457f646" + ] + ], + "versions": [ + "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-05-16T13:58:25.822068" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/tags.yml b/modules/nf-core/gatk4/createsequencedictionary/tests/tags.yml new file mode 100644 index 00000000..035c5e4c --- /dev/null +++ b/modules/nf-core/gatk4/createsequencedictionary/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/createsequencedictionary: + - "modules/nf-core/gatk4/createsequencedictionary/**" diff --git a/modules/nf-core/gatk4/genomicsdbimport/environment.yml b/modules/nf-core/gatk4/genomicsdbimport/environment.yml index a3a13636..55993f44 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/environment.yml +++ b/modules/nf-core/gatk4/genomicsdbimport/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_genomicsdbimport channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test index 9c207b30..5fef5dd2 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test +++ b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test @@ -17,11 +17,11 @@ nextflow_process { """ // [meta, vcf, tbi, interval, interval_value, workspace ] input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) , - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true) , - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) , - [] , - [] ] + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) , + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true) , + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) , + [] , + [] ] // run_intlist input[1] = false // run_updatewspace @@ -36,12 +36,14 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.genomicsdb.get(0).get(1)).list().sort()).match() } //{ assert snapshot(file(process.out.updatedb.get(0).get(1)).list().sort()).match() } //{ assert snapshot(process.out.intervallist.get(0).get(1)).match() } + { assert snapshot( + file(process.out.genomicsdb.get(0).get(1)).list().sort(), + process.out.versions + ).match() } ) } - } test("test_gatk4_genomicsdbimport_get_intervalslist") { @@ -76,10 +78,12 @@ nextflow_process { { assert process.success }, //{ assert snapshot(file(process.out.genomicsdb.get(0).get(1)).list().sort()).match() } //{ assert snapshot(file(process.out.updatedb.get(0).get(1)).list().sort()).match() } - { assert snapshot(process.out.intervallist.get(0).get(1)).match() } + { assert snapshot( + process.out.intervallist.get(0).get(1), + process.out.versions + ).match() } ) } - } test("test_gatk4_genomicsdbimport_update_genomicsdb") { @@ -113,11 +117,13 @@ nextflow_process { assertAll( { assert process.success }, //{ assert snapshot(file(process.out.genomicsdb.get(0).get(1)).list().sort()).match() } - { assert snapshot(file(process.out.updatedb.get(0).get(1)).list().sort()).match() } //{ assert snapshot(process.out.intervallist.get(0).get(1)).match() } + { assert snapshot( + file(process.out.updatedb.get(0).get(1)).list().sort(), + process.out.versions + ).match() } ) } - } test("test_gatk4_genomicsdbimport_stub") { @@ -129,11 +135,11 @@ nextflow_process { """ // [meta, vcf, tbi, interval, interval_value, workspace ] input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) , - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true) , - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) , - [] , - [] ] + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) , + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true) , + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) , + [] , + [] ] // run_intlist input[1] = false // run_updatewspace @@ -147,9 +153,8 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert snapshot(process.out).match()} ) } - } - } diff --git a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap index a633bbdc..55ced0d8 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap @@ -1,40 +1,98 @@ { "test_gatk4_genomicsdbimport_get_intervalslist": { "content": [ - "test.interval_list:md5,4c85812ac15fc1cd29711a851d23c0bf" + "test.interval_list:md5,4c85812ac15fc1cd29711a851d23c0bf", + [ + "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-28T17:55:03.846241" + "timestamp": "2024-07-09T10:42:51.836379" }, "test_gatk4_genomicsdbimport_create_genomicsdb": { "content": [ - "__tiledb_workspace.tdb", - "callset.json", - "chr22$1$40001", - "vcfheader.vcf", - "vidmap.json" + [ + "__tiledb_workspace.tdb", + "callset.json", + "chr22$1$40001", + "vcfheader.vcf", + "vidmap.json" + ], + [ + "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-14T11:22:10.11423157" + "timestamp": "2024-07-09T10:42:36.846239" }, "test_gatk4_genomicsdbimport_update_genomicsdb": { "content": [ - "__tiledb_workspace.tdb", - "callset.json", - "chr22$1$40001", - "vcfheader.vcf", - "vidmap.json" + [ + "__tiledb_workspace.tdb", + "callset.json", + "chr22$1$40001", + "vcfheader.vcf", + "vidmap.json" + ], + [ + "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-14T12:46:42.403794676" + "timestamp": "2024-07-09T10:43:09.00769" + }, + "test_gatk4_genomicsdbimport_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + ], + "genomicsdb": [ + [ + { + "id": "test" + }, + "test:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "intervallist": [ + + ], + "updatedb": [ + + ], + "versions": [ + "versions.yml:md5,c1233a04213021aa66599a36e0fb28cc" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-09T10:43:20.921712" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/genotypegvcfs/environment.yml b/modules/nf-core/gatk4/genotypegvcfs/environment.yml index 6e1b7c04..55993f44 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/environment.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_genotypegvcfs channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/haplotypecaller/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml index d4e8d360..55993f44 100644 --- a/modules/nf-core/gatk4/haplotypecaller/environment.yml +++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_haplotypecaller channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff b/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff deleted file mode 100644 index 72ac552e..00000000 --- a/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff +++ /dev/null @@ -1,30 +0,0 @@ -Changes in module 'nf-core/gatk4/haplotypecaller' -'modules/nf-core/gatk4/haplotypecaller/environment.yml' is unchanged -'modules/nf-core/gatk4/haplotypecaller/meta.yml' is unchanged -Changes in 'gatk4/haplotypecaller/main.nf': ---- modules/nf-core/gatk4/haplotypecaller/main.nf -+++ modules/nf-core/gatk4/haplotypecaller/main.nf -@@ -1,6 +1,6 @@ - process GATK4_HAPLOTYPECALLER { - tag "$meta.id" -- label 'process_medium' -+ label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? -@@ -12,8 +12,8 @@ - tuple val(meta2), path(fasta) - tuple val(meta3), path(fai) - tuple val(meta4), path(dict) -- tuple val(meta5), path(dbsnp) -- tuple val(meta6), path(dbsnp_tbi) -+ path(dbsnp) -+ path(dbsnp_tbi) - - output: - tuple val(meta), path("*.vcf.gz") , emit: vcf - -'modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap' is unchanged -'modules/nf-core/gatk4/haplotypecaller/tests/tags.yml' is unchanged -'modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test' is unchanged -************************************************************ diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index cfb2e190..3043ee07 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -1,6 +1,6 @@ process GATK4_HAPLOTYPECALLER { tag "$meta.id" - label 'process_single' + label 'process_medium' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml index 3d98a08b..315f6dc6 100644 --- a/modules/nf-core/gawk/environment.yml +++ b/modules/nf-core/gawk/environment.yml @@ -1,7 +1,5 @@ -name: gawk channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::gawk=5.3.0 diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml index bcb9d64a..e9379873 100644 --- a/modules/nf-core/mosdepth/environment.yml +++ b/modules/nf-core/mosdepth/environment.yml @@ -1,8 +1,6 @@ -name: mosdepth channels: - conda-forge - bioconda - - defaults dependencies: # renovate: datasource=conda depName=bioconda/mosdepth - mosdepth=0.3.8 diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index a31464c9..f1cd99b0 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,5 @@ -name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::multiqc=1.24.1 diff --git a/modules/nf-core/rtgtools/format/environment.yml b/modules/nf-core/rtgtools/format/environment.yml index 15b3df5b..8aa83cdc 100644 --- a/modules/nf-core/rtgtools/format/environment.yml +++ b/modules/nf-core/rtgtools/format/environment.yml @@ -1,7 +1,5 @@ -name: rtgtools_format channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rtg-tools=3.12.1 diff --git a/modules/nf-core/rtgtools/format/meta.yml b/modules/nf-core/rtgtools/format/meta.yml index 8ed18f54..1991b807 100644 --- a/modules/nf-core/rtgtools/format/meta.yml +++ b/modules/nf-core/rtgtools/format/meta.yml @@ -12,7 +12,7 @@ tools: homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" - licence: "['BSD']" + licence: ["BSD"] input: - meta: type: map diff --git a/modules/nf-core/rtgtools/pedfilter/environment.yml b/modules/nf-core/rtgtools/pedfilter/environment.yml index 62fcaa1c..8aa83cdc 100644 --- a/modules/nf-core/rtgtools/pedfilter/environment.yml +++ b/modules/nf-core/rtgtools/pedfilter/environment.yml @@ -1,7 +1,5 @@ -name: rtgtools_pedfilter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rtg-tools=3.12.1 diff --git a/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff b/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff index 18590bf8..63e0f319 100644 --- a/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff +++ b/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff @@ -1,4 +1,6 @@ Changes in module 'nf-core/rtgtools/pedfilter' +'modules/nf-core/rtgtools/pedfilter/environment.yml' is unchanged +'modules/nf-core/rtgtools/pedfilter/meta.yml' is unchanged Changes in 'rtgtools/pedfilter/main.nf': --- modules/nf-core/rtgtools/pedfilter/main.nf +++ modules/nf-core/rtgtools/pedfilter/main.nf @@ -11,9 +13,7 @@ Changes in 'rtgtools/pedfilter/main.nf': -'modules/nf-core/rtgtools/pedfilter/environment.yml' is unchanged -'modules/nf-core/rtgtools/pedfilter/meta.yml' is unchanged -'modules/nf-core/rtgtools/pedfilter/tests/main.nf.test' is unchanged 'modules/nf-core/rtgtools/pedfilter/tests/main.nf.test.snap' is unchanged 'modules/nf-core/rtgtools/pedfilter/tests/nextflow.config' is unchanged +'modules/nf-core/rtgtools/pedfilter/tests/main.nf.test' is unchanged ************************************************************ diff --git a/modules/nf-core/rtgtools/rocplot/environment.yml b/modules/nf-core/rtgtools/rocplot/environment.yml index 093462a5..8aa83cdc 100644 --- a/modules/nf-core/rtgtools/rocplot/environment.yml +++ b/modules/nf-core/rtgtools/rocplot/environment.yml @@ -1,7 +1,5 @@ -name: rtgtools_rocplot channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rtg-tools=3.12.1 diff --git a/modules/nf-core/rtgtools/vcfeval/environment.yml b/modules/nf-core/rtgtools/vcfeval/environment.yml index e3c64996..8aa83cdc 100644 --- a/modules/nf-core/rtgtools/vcfeval/environment.yml +++ b/modules/nf-core/rtgtools/vcfeval/environment.yml @@ -1,7 +1,5 @@ -name: rtgtools_vcfeval channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rtg-tools=3.12.1 diff --git a/modules/nf-core/rtgtools/vcfeval/meta.yml b/modules/nf-core/rtgtools/vcfeval/meta.yml index f67a35c0..5023ac91 100644 --- a/modules/nf-core/rtgtools/vcfeval/meta.yml +++ b/modules/nf-core/rtgtools/vcfeval/meta.yml @@ -10,7 +10,7 @@ tools: homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" - licence: "['BSD']" + licence: ["BSD"] input: - meta: type: map diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml index 7a95ca61..da2df5e4 100644 --- a/modules/nf-core/samtools/convert/environment.yml +++ b/modules/nf-core/samtools/convert/environment.yml @@ -1,8 +1,6 @@ -name: samtools_convert channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index f8450fa5..b98cbb99 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -1,9 +1,6 @@ -name: samtools_faidx - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 260d516b..da2df5e4 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,8 +1,6 @@ -name: samtools_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml index cd366d6d..da2df5e4 100644 --- a/modules/nf-core/samtools/merge/environment.yml +++ b/modules/nf-core/samtools/merge/environment.yml @@ -1,8 +1,6 @@ -name: samtools_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/snpeff/snpeff/environment.yml b/modules/nf-core/snpeff/snpeff/environment.yml index b492e6a8..f2ad9251 100644 --- a/modules/nf-core/snpeff/snpeff/environment.yml +++ b/modules/nf-core/snpeff/snpeff/environment.yml @@ -1,7 +1,5 @@ -name: snpeff_snpeff channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::snpeff=5.1 diff --git a/modules/nf-core/somalier/extract/environment.yml b/modules/nf-core/somalier/extract/environment.yml index 72397774..d6ce68f6 100644 --- a/modules/nf-core/somalier/extract/environment.yml +++ b/modules/nf-core/somalier/extract/environment.yml @@ -1,7 +1,5 @@ -name: somalier_extract channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::somalier=0.2.19 diff --git a/modules/nf-core/somalier/relate/environment.yml b/modules/nf-core/somalier/relate/environment.yml index 5295646b..d6ce68f6 100644 --- a/modules/nf-core/somalier/relate/environment.yml +++ b/modules/nf-core/somalier/relate/environment.yml @@ -1,7 +1,5 @@ -name: somalier_relate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::somalier=0.2.19 diff --git a/modules/nf-core/somalier/relate/somalier-relate.diff b/modules/nf-core/somalier/relate/somalier-relate.diff index 918d80b2..9e714645 100644 --- a/modules/nf-core/somalier/relate/somalier-relate.diff +++ b/modules/nf-core/somalier/relate/somalier-relate.diff @@ -1,4 +1,6 @@ Changes in module 'nf-core/somalier/relate' +'modules/nf-core/somalier/relate/environment.yml' is unchanged +'modules/nf-core/somalier/relate/meta.yml' is unchanged Changes in 'somalier/relate/main.nf': --- modules/nf-core/somalier/relate/main.nf +++ modules/nf-core/somalier/relate/main.nf @@ -28,9 +30,7 @@ Changes in 'somalier/relate/main.nf': cat <<-END_VERSIONS > versions.yml "${task.process}": -'modules/nf-core/somalier/relate/environment.yml' is unchanged -'modules/nf-core/somalier/relate/meta.yml' is unchanged +'modules/nf-core/somalier/relate/tests/main.nf.test.snap' is unchanged 'modules/nf-core/somalier/relate/tests/tags.yml' is unchanged 'modules/nf-core/somalier/relate/tests/main.nf.test' is unchanged -'modules/nf-core/somalier/relate/tests/main.nf.test.snap' is unchanged ************************************************************ diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml index 56cc0fb1..c863e920 100644 --- a/modules/nf-core/tabix/bgzip/environment.yml +++ b/modules/nf-core/tabix/bgzip/environment.yml @@ -1,8 +1,6 @@ -name: tabix_bgzip channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::tabix=1.11 - bioconda::htslib=1.20 diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml index b9644de9..c863e920 100644 --- a/modules/nf-core/tabix/bgziptabix/environment.yml +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -1,8 +1,6 @@ -name: tabix_bgziptabix channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::tabix=1.11 - bioconda::htslib=1.20 diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index 4d1f9dd4..017c259d 100644 --- a/modules/nf-core/tabix/tabix/environment.yml +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -1,9 +1,6 @@ -name: tabix_tabix - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.20 diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 4f498244..c7794856 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,8 +1,6 @@ -name: untar channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::grep=3.11 - conda-forge::sed=4.8 diff --git a/modules/nf-core/vardictjava/environment.yml b/modules/nf-core/vardictjava/environment.yml index 4e8905e5..a835c6db 100644 --- a/modules/nf-core/vardictjava/environment.yml +++ b/modules/nf-core/vardictjava/environment.yml @@ -1,8 +1,6 @@ -name: vardictjava channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.20 - bioconda::vardict-java=1.8.3 diff --git a/modules/nf-core/vcf2db/environment.yml b/modules/nf-core/vcf2db/environment.yml index 51a8ab8a..58c477f9 100644 --- a/modules/nf-core/vcf2db/environment.yml +++ b/modules/nf-core/vcf2db/environment.yml @@ -1,7 +1,5 @@ -name: vcf2db channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vcf2db=2020.02.24 diff --git a/modules/nf-core/vcfanno/environment.yml b/modules/nf-core/vcfanno/environment.yml index f336cc6b..32c48b15 100644 --- a/modules/nf-core/vcfanno/environment.yml +++ b/modules/nf-core/vcfanno/environment.yml @@ -1,7 +1,5 @@ -name: vcfanno channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vcfanno=0.3.5 diff --git a/modules/nf-core/vcfanno/tests/main.nf.test b/modules/nf-core/vcfanno/tests/main.nf.test index b28431b2..8bbcfd89 100644 --- a/modules/nf-core/vcfanno/tests/main.nf.test +++ b/modules/nf-core/vcfanno/tests/main.nf.test @@ -15,11 +15,11 @@ nextflow_process { """ input[0] = [ [ id:'test_compressed', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists:true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true) ] - input[1] = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml', checkIfExists: true) input[2] = [] input[3] = [ file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz", checkIfExists: true), @@ -45,11 +45,11 @@ nextflow_process { """ input[0] = [ [ id:'test_uncompressed', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), [], - file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists:true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true) ] - input[1] = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml', checkIfExists: true) input[2] = [] input[3] = [ file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz", checkIfExists: true), @@ -77,11 +77,11 @@ nextflow_process { """ input[0] = [ [ id:'test_compressed', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists:true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true) ] - input[1] = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml', checkIfExists: true) input[2] = [] input[3] = [ file("https://github.com/brentp/vcfanno/raw/master/example/exac.vcf.gz", checkIfExists: true), From a27874b9c1a2775d85e0213b90a4b2af97078b06 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 10 Sep 2024 14:21:08 +0200 Subject: [PATCH 32/49] set igenomes ignore to true by default --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 46e627fa..6934047d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -78,7 +78,7 @@ params { // References cmgg_config_base = "/conf/" igenomes_base = null //'s3://ngi-igenomes/igenomes' - igenomes_ignore = false + igenomes_ignore = true genome = "GRCh38" genomes_base = "/references/" genomes_ignore = false From 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 20 Sep 2024 13:18:57 +0200 Subject: [PATCH 33/49] fix tests --- assets/samplesheet.csv | 2 +- main.nf | 1 - .../cram_prepare_samtools_bedtools/main.nf | 10 ++-- subworkflows/local/watchpath_handling/main.nf | 17 +++++- .../cram_call_genotype_gatk4/main.nf.test | 58 +++++++++---------- .../main.nf.test.snap | 37 +++++------- .../local/cram_call_vardictjava/main.nf.test | 32 +++++----- .../cram_call_vardictjava/main.nf.test.snap | 20 +++---- .../main.nf.test | 24 ++++---- .../main.nf.test.snap | 57 +++++++++--------- .../local/input_split_bedtools/main.nf.test | 4 +- .../input_split_bedtools/main.nf.test.snap | 12 ++-- .../local/vcf_annotation/main.nf.test | 4 +- .../local/vcf_annotation/main.nf.test.snap | 8 +-- .../vcf_extract_relate_somalier/main.nf.test | 8 +-- .../main.nf.test.snap | 32 +++++----- .../local/vcf_ped_rtgtools/main.nf.test | 4 +- .../local/vcf_ped_rtgtools/main.nf.test.snap | 8 +-- .../local/vcf_roh_automap/main.nf.test | 4 +- .../local/vcf_roh_automap/main.nf.test.snap | 12 ++-- .../local/vcf_upd_updio/main.nf.test | 8 +-- .../local/vcf_upd_updio/main.nf.test.snap | 8 +-- .../vcf_validate_small_variants/main.nf.test | 4 +- .../main.nf.test.snap | 40 ++++++------- 24 files changed, 210 insertions(+), 204 deletions(-) diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index b20e3926..2f8a87d7 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,4 +1,4 @@ sample,family,cram,crai,roi,ped,truth_vcf,truth_tbi,truth_bed,vardict_min_af NA24143,Proband_12345,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24143.cram,,,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/genome/test.ped,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24143.vcf.gz,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24143.vcf.gz.tbi,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/regions/roi.bed,0.01 NA24149,Proband_12345,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24149.cram,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24149.cram.crai,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/regions/roi.bed,,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24149.vcf.gz,,, -NA24385,Proband_12345,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24385.cram,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24385.cram.crai,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/regions/roi.bed,,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24385.vcf.gz,,, +NA24149,Proband_12345,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24385.cram,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24385.cram.crai,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/regions/roi.bed,,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24385.vcf.gz,,, diff --git a/main.nf b/main.nf index 823c6263..44089aa8 100644 --- a/main.nf +++ b/main.nf @@ -194,7 +194,6 @@ workflow { def multiqc_logo = params.multiqc_logo ?: "$projectDir/assets/CMGG_logo.png" - print(params.genomes) // // SUBWORKFLOW: Run initialisation tasks // diff --git a/subworkflows/local/cram_prepare_samtools_bedtools/main.nf b/subworkflows/local/cram_prepare_samtools_bedtools/main.nf index 3be4dab3..94e24a7c 100644 --- a/subworkflows/local/cram_prepare_samtools_bedtools/main.nf +++ b/subworkflows/local/cram_prepare_samtools_bedtools/main.nf @@ -37,9 +37,9 @@ workflow CRAM_PREPARE_SAMTOOLS_BEDTOOLS { .groupTuple() .branch { meta, cram, crai -> multiple: cram.size() > 1 - return [meta, cram] + return [meta.target, cram] single: cram.size() == 1 - return [meta, cram[0], crai[0]] + return [meta.target, cram[0], crai[0]] } .set { ch_cram_branch } @@ -104,9 +104,9 @@ workflow CRAM_PREPARE_SAMTOOLS_BEDTOOLS { } } found: is_present - return [ meta, output_roi ] + return [ meta.target, output_roi ] missing: !is_present - return [ meta, [] ] + return [ meta.target, [] ] } .set { ch_roi_branch } @@ -135,7 +135,7 @@ workflow CRAM_PREPARE_SAMTOOLS_BEDTOOLS { .groupTuple() .combine(MERGE_ROI_PARAMS.out.bed.map { meta, bed -> bed }) .map { meta, missing, default_roi -> - [ meta, default_roi ] + [ meta.target, default_roi ] } .set { ch_missing_rois } } else { diff --git a/subworkflows/local/watchpath_handling/main.nf b/subworkflows/local/watchpath_handling/main.nf index 5e96ec58..88cf3fbc 100644 --- a/subworkflows/local/watchpath_handling/main.nf +++ b/subworkflows/local/watchpath_handling/main.nf @@ -31,6 +31,7 @@ workflow WATCHPATH_HANDLING { def families = [:] def sample_counts = [:] + def sample_metas = [:] // Determine which files to watch for def samplesheet_list = samplesheetToList(input_samplesheet, samplesheet_schema) @@ -71,8 +72,19 @@ workflow WATCHPATH_HANDLING { if (!sample_counts.containsKey(sample_id)) { sample_counts[sample_id] = 1 + sample_metas[sample_id] = row[0] } else { sample_counts[sample_id] += 1 + if(sample_metas[sample_id] != row[0]) { + def other_meta = sample_metas[sample_id] + def diff_keys = [] + other_meta.each { k,v -> + if (v != row[0][k]) { + diff_keys.add(k) + } + } + errors.add("Found multiple entries for sample '${sample_id}' in the samplesheet with differing meta values (`${diff_keys.join(' ')}`).") + } } def new_meta = row[0] + [family:family] @@ -81,13 +93,14 @@ workflow WATCHPATH_HANDLING { return row } + // Stop the pipeline if extra validation errors have been detected if (errors.size() > 0) { error(errors.join("\n")) } Channel.fromList(samplesheet_list).set { ch_samplesheet_all } - if (watchdir) { + if (watchdir && expected_files.size() > 1) { watchdir_path = file(watchdir) if (!watchdir_path.exists()) { @@ -148,7 +161,7 @@ workflow WATCHPATH_HANDLING { duplicate_count:sample_counts[row[0].id] ] return row - }.view() + } .set { samplesheet } emit: diff --git a/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test b/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test index 33425c77..37eca413 100644 --- a/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test +++ b/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test @@ -21,17 +21,17 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24143.00001", sample:"NA24143", family:"Ashkenazim", family_count:1, split_count:3], + [id:"NA24143.00001", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", split_count:3], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true), file(params.split1, checkIfExists:true) ],[ - [id:"NA24143.00002", sample:"NA24143", family:"Ashkenazim", family_count:1, split_count:3], + [id:"NA24143.00002", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", split_count:3], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true), file(params.split2, checkIfExists:true) ],[ - [id:"NA24143.00003", sample:"NA24143", family:"Ashkenazim", family_count:1, split_count:3], + [id:"NA24143.00003", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", split_count:3], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true), file(params.split3, checkIfExists:true) @@ -86,7 +86,7 @@ nextflow_workflow { """ input[0] = Channel.empty() input[1] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:1], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143"], file(params.gvcf1, checkIfExists:true), file(params.gtbi1, checkIfExists:true) ]) @@ -138,27 +138,27 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24835.00001", sample:"NA24835", family:"Ashkenazim", family_count:3, split_count:3], + [id:"NA24835.00001", sample:"NA24835", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", split_count:3], file(params.cram3, checkIfExists:true), file(params.crai3, checkIfExists:true), file(params.split1, checkIfExists:true) ],[ - [id:"NA24835.00002", sample:"NA24835", family:"Ashkenazim", family_count:3, split_count:3], + [id:"NA24835.00002", sample:"NA24835", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", split_count:3], file(params.cram3, checkIfExists:true), file(params.crai3, checkIfExists:true), file(params.split2, checkIfExists:true) ],[ - [id:"NA24835.00003", sample:"NA24835", family:"Ashkenazim", family_count:3, split_count:3], + [id:"NA24835.00003", sample:"NA24835", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", split_count:3], file(params.cram3, checkIfExists:true), file(params.crai3, checkIfExists:true), file(params.split3, checkIfExists:true) ]) input[1] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:3], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385"], file(params.gvcf1, checkIfExists:true), file(params.gtbi1, checkIfExists:true) ],[ - [id:"NA24149", sample:"NA24149", family:"Ashkenazim", family_count:3], + [id:"NA24149", sample:"NA24149", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385"], file(params.gvcf2, checkIfExists:true), file(params.gtbi2, checkIfExists:true) ]) @@ -211,27 +211,27 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24835.00001", sample:"NA24835", family:"Ashkenazim", family_count:3, split_count:3], + [id:"NA24835.00001", sample:"NA24835", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", split_count:3], file(params.cram3, checkIfExists:true), file(params.crai3, checkIfExists:true), file(params.split1, checkIfExists:true) ],[ - [id:"NA24835.00002", sample:"NA24835", family:"Ashkenazim", family_count:3, split_count:3], + [id:"NA24835.00002", sample:"NA24835", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", split_count:3], file(params.cram3, checkIfExists:true), file(params.crai3, checkIfExists:true), file(params.split2, checkIfExists:true) ],[ - [id:"NA24835.00003", sample:"NA24835", family:"Ashkenazim", family_count:3, split_count:3], + [id:"NA24835.00003", sample:"NA24835", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", split_count:3], file(params.cram3, checkIfExists:true), file(params.crai3, checkIfExists:true), file(params.split3, checkIfExists:true) ]) input[1] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:3], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385"], file(params.gvcf1, checkIfExists:true), file(params.gtbi1, checkIfExists:true) ],[ - [id:"NA24149", sample:"NA24149", family:"Ashkenazim", family_count:3], + [id:"NA24149", sample:"NA24149", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385"], file(params.gvcf2, checkIfExists:true), file(params.gtbi2, checkIfExists:true) ]) @@ -284,27 +284,27 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24835.00001", sample:"NA24835", family:"Ashkenazim", family_count:3, split_count:3], + [id:"NA24835.00001", sample:"NA24835", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", split_count:3], file(params.cram3, checkIfExists:true), file(params.crai3, checkIfExists:true), file(params.split1, checkIfExists:true) ],[ - [id:"NA24835.00002", sample:"NA24835", family:"Ashkenazim", family_count:3, split_count:3], + [id:"NA24835.00002", sample:"NA24835", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", split_count:3], file(params.cram3, checkIfExists:true), file(params.crai3, checkIfExists:true), file(params.split2, checkIfExists:true) ],[ - [id:"NA24835.00003", sample:"NA24835", family:"Ashkenazim", family_count:3, split_count:3], + [id:"NA24835.00003", sample:"NA24835", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", split_count:3], file(params.cram3, checkIfExists:true), file(params.crai3, checkIfExists:true), file(params.split3, checkIfExists:true) ]) input[1] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:3], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385"], file(params.gvcf1, checkIfExists:true), file(params.gtbi1, checkIfExists:true) ],[ - [id:"NA24149", sample:"NA24149", family:"Ashkenazim", family_count:3], + [id:"NA24149", sample:"NA24149", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385"], file(params.gvcf2, checkIfExists:true), file(params.gtbi2, checkIfExists:true) ]) @@ -357,27 +357,27 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24835.00001", sample:"NA24835", family:"Ashkenazim", family_count:3, split_count:3], + [id:"NA24835.00001", sample:"NA24835", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", split_count:3], file(params.cram3, checkIfExists:true), file(params.crai3, checkIfExists:true), file(params.split1, checkIfExists:true) ],[ - [id:"NA24835.00002", sample:"NA24835", family:"Ashkenazim", family_count:3, split_count:3], + [id:"NA24835.00002", sample:"NA24835", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", split_count:3], file(params.cram3, checkIfExists:true), file(params.crai3, checkIfExists:true), file(params.split2, checkIfExists:true) ],[ - [id:"NA24835.00003", sample:"NA24835", family:"Ashkenazim", family_count:3, split_count:3], + [id:"NA24835.00003", sample:"NA24835", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", split_count:3], file(params.cram3, checkIfExists:true), file(params.crai3, checkIfExists:true), file(params.split3, checkIfExists:true) ]) input[1] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:3], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385"], file(params.gvcf1, checkIfExists:true), file(params.gtbi1, checkIfExists:true) ],[ - [id:"NA24149", sample:"NA24149", family:"Ashkenazim", family_count:3], + [id:"NA24149", sample:"NA24149", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385"], file(params.gvcf2, checkIfExists:true), file(params.gtbi2, checkIfExists:true) ]) @@ -429,27 +429,27 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24835.00001", sample:"NA24835", family:"Ashkenazim", family_count:2, split_count:3], + [id:"NA24835.00001", sample:"NA24835", family:"Ashkenazim", family_samples:"NA24149,NA24385", split_count:3], file(params.cram3, checkIfExists:true), file(params.crai3, checkIfExists:true), file(params.split1, checkIfExists:true) ],[ - [id:"NA24835.00002", sample:"NA24835", family:"Ashkenazim", family_count:2, split_count:3], + [id:"NA24835.00002", sample:"NA24835", family:"Ashkenazim", family_samples:"NA24149,NA24385", split_count:3], file(params.cram3, checkIfExists:true), file(params.crai3, checkIfExists:true), file(params.split2, checkIfExists:true) ],[ - [id:"NA24835.00003", sample:"NA24835", family:"Ashkenazim", family_count:2, split_count:3], + [id:"NA24835.00003", sample:"NA24835", family:"Ashkenazim", family_samples:"NA24149,NA24385", split_count:3], file(params.cram3, checkIfExists:true), file(params.crai3, checkIfExists:true), file(params.split3, checkIfExists:true) ]) input[1] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:2], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143"], file(params.gvcf1, checkIfExists:true), file(params.gtbi1, checkIfExists:true) ],[ - [id:"NA24149", sample:"NA24149", family:"NA24149", family_count:2], + [id:"NA24149", sample:"NA24149", family:"NA24149", family_samples:"NA24149,NA24385"], file(params.gvcf2, checkIfExists:true), file(params.gtbi2, checkIfExists:true) ]) diff --git a/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap b/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap index 6c932f93..a0aec425 100644 --- a/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap +++ b/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap @@ -22,10 +22,9 @@ [ { "family": "Ashkenazim", - "id": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "caller": "haplotypecaller", - "samples": "NA24143,NA24149,NA24835" + "id": "Ashkenazim" }, "Ashkenazim.haplotypecaller.vcf.gz", "Ashkenazim.haplotypecaller.vcf.gz.tbi" @@ -41,7 +40,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-05T11:18:02.353352239" + "timestamp": "2024-09-05T17:35:02.44674969" }, "filter - family": { "content": [ @@ -49,10 +48,9 @@ [ { "family": "Ashkenazim", - "id": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "caller": "haplotypecaller", - "samples": "NA24143,NA24149,NA24835" + "id": "Ashkenazim" }, "Ashkenazim.haplotypecaller.vcf.gz", "Ashkenazim.haplotypecaller.vcf.gz.tbi" @@ -68,7 +66,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-05T11:19:14.883570897" + "timestamp": "2024-09-05T17:35:46.768542501" }, "default - gvcfs": { "content": [ @@ -76,10 +74,9 @@ [ { "family": "Ashkenazim", - "id": "Ashkenazim", - "family_count": 1, + "family_samples": "NA24143", "caller": "haplotypecaller", - "samples": "NA24143" + "id": "Ashkenazim" }, "Ashkenazim.haplotypecaller.vcf.gz", "Ashkenazim.haplotypecaller.vcf.gz.tbi" @@ -91,9 +88,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-06T12:56:23.435795439" + "timestamp": "2024-09-05T17:34:17.846266913" }, "default - crams": { "content": [ @@ -101,10 +98,9 @@ [ { "family": "Ashkenazim", - "id": "Ashkenazim", - "family_count": 1, + "family_samples": "NA24143", "caller": "haplotypecaller", - "samples": "NA24143" + "id": "Ashkenazim" }, "Ashkenazim.haplotypecaller.vcf.gz", "Ashkenazim.haplotypecaller.vcf.gz.tbi" @@ -120,7 +116,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-05T11:16:25.448441115" + "timestamp": "2024-09-05T17:33:52.045772718" }, "only_call - family": { "content": [ @@ -145,10 +141,9 @@ [ { "family": "Ashkenazim", - "id": "Ashkenazim", - "family_count": 2, + "family_samples": "NA24143", "caller": "haplotypecaller", - "samples": "NA24143,NA24835" + "id": "Ashkenazim" }, "Ashkenazim.haplotypecaller.vcf.gz", "Ashkenazim.haplotypecaller.vcf.gz.tbi" @@ -164,6 +159,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-05T11:21:57.601081087" + "timestamp": "2024-09-06T14:26:29.249708339" } } \ No newline at end of file diff --git a/tests/subworkflows/local/cram_call_vardictjava/main.nf.test b/tests/subworkflows/local/cram_call_vardictjava/main.nf.test index b0914d97..05798304 100644 --- a/tests/subworkflows/local/cram_call_vardictjava/main.nf.test +++ b/tests/subworkflows/local/cram_call_vardictjava/main.nf.test @@ -20,22 +20,22 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:1], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143"], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true) ]) input[1] = Channel.of([ - [id:"NA24143.00001", sample:"NA24143", family:"Ashkenazim", family_count:1, split_count:3], + [id:"NA24143.00001", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", split_count:3], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true), file(params.split1, checkIfExists:true) ],[ - [id:"NA24143.00002", sample:"NA24143", family:"Ashkenazim", family_count:1, split_count:3], + [id:"NA24143.00002", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", split_count:3], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true), file(params.split2, checkIfExists:true) ],[ - [id:"NA24143.00003", sample:"NA24143", family:"Ashkenazim", family_count:1, split_count:3], + [id:"NA24143.00003", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", split_count:3], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true), file(params.split3, checkIfExists:true) @@ -77,22 +77,22 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:1], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143"], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true) ]) input[1] = Channel.of([ - [id:"NA24143.00001", sample:"NA24143", family:"Ashkenazim", family_count:1, split_count:3], + [id:"NA24143.00001", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", split_count:3], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true), file(params.split1, checkIfExists:true) ],[ - [id:"NA24143.00002", sample:"NA24143", family:"Ashkenazim", family_count:1, split_count:3], + [id:"NA24143.00002", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", split_count:3], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true), file(params.split2, checkIfExists:true) ],[ - [id:"NA24143.00003", sample:"NA24143", family:"Ashkenazim", family_count:1, split_count:3], + [id:"NA24143.00003", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", split_count:3], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true), file(params.split3, checkIfExists:true) @@ -133,41 +133,41 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:2], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143,NA24149"], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true) ],[ - [id:"NA24149", sample:"NA24149", family:"Ashkenazim", family_count:2], + [id:"NA24149", sample:"NA24149", family:"Ashkenazim", family_samples:"NA24143,NA24149"], file(params.cram2, checkIfExists:true), file(params.crai2, checkIfExists:true) ]) input[1] = Channel.of([ - [id:"NA24143.00001", sample:"NA24143", family:"Ashkenazim", family_count:2, split_count:3], + [id:"NA24143.00001", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143,NA24149", split_count:3], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true), file(params.split1, checkIfExists:true) ],[ - [id:"NA24143.00002", sample:"NA24143", family:"Ashkenazim", family_count:2, split_count:3], + [id:"NA24143.00002", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143,NA24149", split_count:3], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true), file(params.split2, checkIfExists:true) ],[ - [id:"NA24143.00003", sample:"NA24143", family:"Ashkenazim", family_count:2, split_count:3], + [id:"NA24143.00003", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143,NA24149", split_count:3], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true), file(params.split3, checkIfExists:true) ],[ - [id:"NA24149.00001", sample:"NA24149", family:"Ashkenazim", family_count:2, split_count:3], + [id:"NA24149.00001", sample:"NA24149", family:"Ashkenazim", family_samples:"NA24143,NA24149", split_count:3], file(params.cram2, checkIfExists:true), file(params.crai2, checkIfExists:true), file(params.split1, checkIfExists:true) ],[ - [id:"NA24149.00002", sample:"NA24149", family:"Ashkenazim", family_count:2, split_count:3], + [id:"NA24149.00002", sample:"NA24149", family:"Ashkenazim", family_samples:"NA24143,NA24149", split_count:3], file(params.cram2, checkIfExists:true), file(params.crai2, checkIfExists:true), file(params.split2, checkIfExists:true) ],[ - [id:"NA24149.00003", sample:"NA24149", family:"Ashkenazim", family_count:2, split_count:3], + [id:"NA24149.00003", sample:"NA24149", family:"Ashkenazim", family_samples:"NA24143,NA24149", split_count:3], file(params.cram2, checkIfExists:true), file(params.crai2, checkIfExists:true), file(params.split3, checkIfExists:true) diff --git a/tests/subworkflows/local/cram_call_vardictjava/main.nf.test.snap b/tests/subworkflows/local/cram_call_vardictjava/main.nf.test.snap index 8cbbdb2e..f2057a7b 100644 --- a/tests/subworkflows/local/cram_call_vardictjava/main.nf.test.snap +++ b/tests/subworkflows/local/cram_call_vardictjava/main.nf.test.snap @@ -7,7 +7,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 1, + "family_samples": "NA24143", "caller": "vardict", "samples": "NA24143" }, @@ -18,9 +18,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-06T13:05:31.562298546" + "timestamp": "2024-09-05T17:38:01.461442987" }, "default": { "content": [ @@ -30,7 +30,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 1, + "family_samples": "NA24143", "caller": "vardict", "samples": "NA24143" }, @@ -41,9 +41,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-06T13:05:04.322416692" + "timestamp": "2024-09-05T17:37:40.178107639" }, "family": { "content": [ @@ -53,7 +53,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 2, + "family_samples": "NA24143,NA24149", "caller": "vardict", "samples": "NA24143" }, @@ -65,7 +65,7 @@ "id": "NA24149", "sample": "NA24149", "family": "Ashkenazim", - "family_count": 2, + "family_samples": "NA24143,NA24149", "caller": "vardict", "samples": "NA24149" }, @@ -76,8 +76,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-06T13:06:05.012625054" + "timestamp": "2024-09-05T17:38:29.203806206" } } \ No newline at end of file diff --git a/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test b/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test index 7c6c226c..472a1eae 100644 --- a/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test +++ b/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test @@ -14,12 +14,12 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:1], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", duplicate_count:1], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true) ]) input[1] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:1], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", duplicate_count:1], [] ]) input[2] = Channel.value([ @@ -54,12 +54,12 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:1], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", duplicate_count:1], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true) ]) input[1] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:1], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", duplicate_count:1], [] ]) input[2] = Channel.value([ @@ -94,12 +94,12 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:1], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", duplicate_count:1], file(params.cram1, checkIfExists:true), [] ]) input[1] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:1], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", duplicate_count:1], file(params.bed, checkIfExists:true) ]) input[2] = Channel.value([ @@ -134,16 +134,16 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:1], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", duplicate_count:2], file(params.cram1, checkIfExists:true), - file(params.crai1, checkIfExists:true) + [] ],[ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:1], - file(params.cram1, checkIfExists:true), - file(params.crai1, checkIfExists:true) + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", duplicate_count:2], + file(params.cram2, checkIfExists:true), + [] ]) input[1] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:1], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", duplicate_count:2], file(params.bed, checkIfExists:true) ]) input[2] = Channel.value([ diff --git a/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test.snap b/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test.snap index d19744ac..47b214c1 100644 --- a/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test.snap +++ b/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test.snap @@ -7,32 +7,25 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 1 + "family_samples": "NA24143", + "duplicate_count": 2 }, - 899520, + 798258, "NA24143.cram.crai" ] ], [ - [ - { - "id": "NA24143", - "sample": "NA24143", - "family": "Ashkenazim", - "family_count": 1 - }, - "NA24143_intersect.bed:md5,b87069698afefb15282d069e56110046" - ] + ], [ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-04T17:01:48.046624445" + "timestamp": "2024-09-06T14:40:18.974586888" }, "default - WGS": { "content": [ @@ -42,7 +35,8 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 1 + "family_samples": "NA24143", + "duplicate_count": 1 }, "NA24143.cram", "NA24143.cram.crai" @@ -54,7 +48,8 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 1 + "family_samples": "NA24143", + "duplicate_count": 1 }, "NA24143.filter.bed:md5,9fc0cc2e4403678f18bc8b18646abd66" ] @@ -64,10 +59,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T10:49:45.063311741" + "timestamp": "2024-09-06T14:32:19.290286542" }, "default - WES": { "content": [ @@ -77,7 +72,8 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 1 + "family_samples": "NA24143", + "duplicate_count": 1 }, "NA24143.cram", "NA24143.cram.crai" @@ -89,7 +85,8 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 1 + "family_samples": "NA24143", + "duplicate_count": 1 }, "NA24143_intersect.bed:md5,b87069698afefb15282d069e56110046" ] @@ -99,10 +96,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T11:02:27.487076852" + "timestamp": "2024-09-06T14:33:15.988619426" }, "default - WES common ROI": { "content": [ @@ -112,7 +109,8 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 1 + "family_samples": "NA24143", + "duplicate_count": 1 }, "NA24143.cram", "NA24143.cram.crai" @@ -124,7 +122,8 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 1 + "family_samples": "NA24143", + "duplicate_count": 1 }, "NA24143_intersect.bed:md5,b87069698afefb15282d069e56110046" ] @@ -134,9 +133,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T11:02:14.280224701" + "timestamp": "2024-09-06T14:32:49.756585296" } } \ No newline at end of file diff --git a/tests/subworkflows/local/input_split_bedtools/main.nf.test b/tests/subworkflows/local/input_split_bedtools/main.nf.test index 3c9507ca..87cc55a6 100644 --- a/tests/subworkflows/local/input_split_bedtools/main.nf.test +++ b/tests/subworkflows/local/input_split_bedtools/main.nf.test @@ -14,12 +14,12 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:1], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143"], file(params.bed, checkIfExists:true), 3 ]) input[1] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:1], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143"], file(params.cram1, checkIfExists:true), file(params.crai1, checkIfExists:true), ]) diff --git a/tests/subworkflows/local/input_split_bedtools/main.nf.test.snap b/tests/subworkflows/local/input_split_bedtools/main.nf.test.snap index 9f34f75c..6089d29e 100644 --- a/tests/subworkflows/local/input_split_bedtools/main.nf.test.snap +++ b/tests/subworkflows/local/input_split_bedtools/main.nf.test.snap @@ -7,7 +7,7 @@ "id": "NA24143.00001", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 1, + "family_samples": "NA24143", "split_count": 3 }, "NA24143.cram", @@ -19,7 +19,7 @@ "id": "NA24143.00002", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 1, + "family_samples": "NA24143", "split_count": 3 }, "NA24143.cram", @@ -31,7 +31,7 @@ "id": "NA24143.00003", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 1, + "family_samples": "NA24143", "split_count": 3 }, "NA24143.cram", @@ -41,9 +41,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T11:15:19.235405576" + "timestamp": "2024-09-05T17:39:07.719231196" } } \ No newline at end of file diff --git a/tests/subworkflows/local/vcf_annotation/main.nf.test b/tests/subworkflows/local/vcf_annotation/main.nf.test index b829d298..99cedb8e 100644 --- a/tests/subworkflows/local/vcf_annotation/main.nf.test +++ b/tests/subworkflows/local/vcf_annotation/main.nf.test @@ -19,7 +19,7 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24143", family:"NA24143", family_count:1, caller:"haplotypecaller"], + [id:"NA24143", family:"NA24143", family_samples:"NA24143", caller:"haplotypecaller"], file(params.vcf1, checkIfExists:true) ]) input[1] = Channel.value([ @@ -66,7 +66,7 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24143", family:"NA24143", family_count:1, caller:"haplotypecaller"], + [id:"NA24143", family:"NA24143", family_samples:"NA24143", caller:"haplotypecaller"], file(params.vcf1, checkIfExists:true) ]) input[1] = Channel.value([ diff --git a/tests/subworkflows/local/vcf_annotation/main.nf.test.snap b/tests/subworkflows/local/vcf_annotation/main.nf.test.snap index 12d0ef2c..d3ebc487 100644 --- a/tests/subworkflows/local/vcf_annotation/main.nf.test.snap +++ b/tests/subworkflows/local/vcf_annotation/main.nf.test.snap @@ -6,7 +6,7 @@ { "id": "NA24143", "family": "NA24143", - "family_count": 1, + "family_samples": "NA24143", "caller": "haplotypecaller" }, "NA24143.haplotypecaller.vcf.gz" @@ -22,7 +22,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-05T12:53:05.739638954" + "timestamp": "2024-09-05T17:39:23.107888975" }, "vcfanno": { "content": [ @@ -31,7 +31,7 @@ { "id": "NA24143", "family": "NA24143", - "family_count": 1, + "family_samples": "NA24143", "caller": "haplotypecaller" }, "NA24143.haplotypecaller.vcf.gz" @@ -47,6 +47,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-05T12:53:27.894947052" + "timestamp": "2024-09-05T17:39:39.640344999" } } \ No newline at end of file diff --git a/tests/subworkflows/local/vcf_extract_relate_somalier/main.nf.test b/tests/subworkflows/local/vcf_extract_relate_somalier/main.nf.test index a07570e9..3e277b57 100644 --- a/tests/subworkflows/local/vcf_extract_relate_somalier/main.nf.test +++ b/tests/subworkflows/local/vcf_extract_relate_somalier/main.nf.test @@ -14,7 +14,7 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller"], + [id:"Ashkenazim", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", caller:"haplotypecaller"], file(params.famvcf, checkIfExists:true), file(params.famtbi, checkIfExists:true) ]) @@ -22,7 +22,7 @@ nextflow_workflow { input[2] = Channel.value([[id:"ref"], file(params.fai, checkIfExists:true)]) input[3] = Channel.value([[id:"ref"], file(params.somalier_sites, checkIfExists:true)]) input[4] = Channel.of([ - [id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller"], + [id:"Ashkenazim", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", caller:"haplotypecaller"], file(params.ped, checkIfExists:true) ]) """ @@ -50,7 +50,7 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller"], + [id:"Ashkenazim", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", caller:"haplotypecaller"], file(params.famvcf, checkIfExists:true), file(params.famtbi, checkIfExists:true) ]) @@ -58,7 +58,7 @@ nextflow_workflow { input[2] = Channel.value([[id:"ref"], file(params.fai, checkIfExists:true)]) input[3] = Channel.value([[id:"ref"], file(params.somalier_sites, checkIfExists:true)]) input[4] = Channel.of([ - [id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller"], + [id:"Ashkenazim", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", caller:"haplotypecaller"], [] ]) """ diff --git a/tests/subworkflows/local/vcf_extract_relate_somalier/main.nf.test.snap b/tests/subworkflows/local/vcf_extract_relate_somalier/main.nf.test.snap index 6f69f1f5..49d14e7c 100644 --- a/tests/subworkflows/local/vcf_extract_relate_somalier/main.nf.test.snap +++ b/tests/subworkflows/local/vcf_extract_relate_somalier/main.nf.test.snap @@ -6,7 +6,7 @@ { "id": "Ashkenazim", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "caller": "haplotypecaller" }, [ @@ -21,7 +21,7 @@ { "id": "Ashkenazim", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "caller": "haplotypecaller" }, "Ashkenazim.haplotypecaller.html:md5,a7cc550571c8543643d10b2e9db68a48" @@ -32,7 +32,7 @@ { "id": "Ashkenazim", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "caller": "haplotypecaller" }, "Ashkenazim.haplotypecaller.pairs.tsv:md5,0c89abf63de67c9f0ee931e883a17a66" @@ -43,7 +43,7 @@ { "id": "Ashkenazim", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "caller": "haplotypecaller" }, "Ashkenazim.haplotypecaller.samples.tsv:md5,26e108afb44bcbaf4c47e43eb5611d15" @@ -54,7 +54,7 @@ { "id": "Ashkenazim", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "caller": "haplotypecaller" }, "Ashkenazim.haplotypecaller_somalier.ped:md5,689bb83118511ddcb09ae6d30d2d99b3" @@ -62,10 +62,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T13:17:18.055689163" + "timestamp": "2024-09-05T17:39:52.526057891" }, "default - no peds": { "content": [ @@ -74,7 +74,7 @@ { "id": "Ashkenazim", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "caller": "haplotypecaller" }, [ @@ -89,7 +89,7 @@ { "id": "Ashkenazim", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "caller": "haplotypecaller" }, "Ashkenazim.haplotypecaller.html:md5,1622292889a889778f10ae037c051e44" @@ -100,7 +100,7 @@ { "id": "Ashkenazim", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "caller": "haplotypecaller" }, "Ashkenazim.haplotypecaller.pairs.tsv:md5,fc51248691992f10a6b5176f5a2d6231" @@ -111,7 +111,7 @@ { "id": "Ashkenazim", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "caller": "haplotypecaller" }, "Ashkenazim.haplotypecaller.samples.tsv:md5,1c12b44787ba9bc79943737fa54d3007" @@ -122,7 +122,7 @@ { "id": "Ashkenazim", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "caller": "haplotypecaller" }, "Ashkenazim.haplotypecaller_somalier.ped:md5,f1a0cb22a941d0563fae2ca3c30dd0d4" @@ -130,9 +130,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T13:17:29.504749349" + "timestamp": "2024-09-05T17:40:03.603049023" } } \ No newline at end of file diff --git a/tests/subworkflows/local/vcf_ped_rtgtools/main.nf.test b/tests/subworkflows/local/vcf_ped_rtgtools/main.nf.test index 71fe4235..24398ed4 100644 --- a/tests/subworkflows/local/vcf_ped_rtgtools/main.nf.test +++ b/tests/subworkflows/local/vcf_ped_rtgtools/main.nf.test @@ -17,12 +17,12 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller"], + [id:"Ashkenazim", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", caller:"haplotypecaller"], file(params.famvcf, checkIfExists:true), file(params.famtbi, checkIfExists:true) ]) input[1] = Channel.of([ - [id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller"], + [id:"Ashkenazim", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", caller:"haplotypecaller"], file(params.ped, checkIfExists:true) ]) """ diff --git a/tests/subworkflows/local/vcf_ped_rtgtools/main.nf.test.snap b/tests/subworkflows/local/vcf_ped_rtgtools/main.nf.test.snap index b5d831e0..f988cc9f 100644 --- a/tests/subworkflows/local/vcf_ped_rtgtools/main.nf.test.snap +++ b/tests/subworkflows/local/vcf_ped_rtgtools/main.nf.test.snap @@ -6,7 +6,7 @@ { "id": "Ashkenazim", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "caller": "haplotypecaller" }, "Ashkenazim.haplotypecaller.vcf.gz" @@ -14,9 +14,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T17:28:32.40423584" + "timestamp": "2024-09-05T17:40:15.516745396" } } \ No newline at end of file diff --git a/tests/subworkflows/local/vcf_roh_automap/main.nf.test b/tests/subworkflows/local/vcf_roh_automap/main.nf.test index b73cbbfd..724b1757 100644 --- a/tests/subworkflows/local/vcf_roh_automap/main.nf.test +++ b/tests/subworkflows/local/vcf_roh_automap/main.nf.test @@ -18,7 +18,7 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller", samples: "NA24143,NA24835,NA24149"], + [id:"Ashkenazim", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", caller:"haplotypecaller", samples: "NA24143,NA24835,NA24149"], file(params.famvcf, checkIfExists:true), file(params.famtbi, checkIfExists:true) ]) @@ -58,7 +58,7 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24143", family:"NA24143", family_count:1, caller:"haplotypecaller", samples: "NA24143,NA24835,NA24149"], + [id:"NA24143", family:"NA24143", family_samples:"NA24143", caller:"haplotypecaller", samples: "NA24143,NA24835,NA24149"], file(params.vcf1, checkIfExists:true), file(params.tbi1, checkIfExists:true) ]) diff --git a/tests/subworkflows/local/vcf_roh_automap/main.nf.test.snap b/tests/subworkflows/local/vcf_roh_automap/main.nf.test.snap index 60f01c03..cc008cf9 100644 --- a/tests/subworkflows/local/vcf_roh_automap/main.nf.test.snap +++ b/tests/subworkflows/local/vcf_roh_automap/main.nf.test.snap @@ -6,7 +6,7 @@ { "id": "Ashkenazim", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "caller": "haplotypecaller", "samples": "NA24143,NA24835,NA24149" }, @@ -26,9 +26,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-06T13:06:37.322068108" + "timestamp": "2024-09-05T17:40:27.65975553" }, "default - sample": { "content": [ @@ -37,7 +37,7 @@ { "id": "NA24143", "family": "NA24143", - "family_count": 1, + "family_samples": "NA24143", "caller": "haplotypecaller", "samples": "NA24143,NA24835,NA24149" }, @@ -52,8 +52,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-06T13:06:47.205904762" + "timestamp": "2024-09-05T17:40:37.637175166" } } \ No newline at end of file diff --git a/tests/subworkflows/local/vcf_upd_updio/main.nf.test b/tests/subworkflows/local/vcf_upd_updio/main.nf.test index 226c71a1..1507c48a 100644 --- a/tests/subworkflows/local/vcf_upd_updio/main.nf.test +++ b/tests/subworkflows/local/vcf_upd_updio/main.nf.test @@ -17,12 +17,12 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller"], + [id:"Ashkenazim", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", caller:"haplotypecaller"], file(params.famvcf, checkIfExists:true), file(params.famtbi, checkIfExists:true) ]) input[1] = Channel.of([ - [id:"Ashkenazim", family:"Ashkenazim", family_count:3, caller:"haplotypecaller"], + [id:"Ashkenazim", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385", caller:"haplotypecaller"], file(params.ped, checkIfExists:true) ]) input[2] = [[],[]] @@ -50,12 +50,12 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"Ashkenazim", family:"Ashkenazim", family_count:1, caller:"haplotypecaller"], + [id:"Ashkenazim", family:"Ashkenazim", family_samples:"NA24143", caller:"haplotypecaller"], file(params.vcf1, checkIfExists:true), file(params.tbi1, checkIfExists:true) ]) input[1] = Channel.of([ - [id:"Ashkenazim", family:"Ashkenazim", family_count:1, caller:"haplotypecaller"], + [id:"Ashkenazim", family:"Ashkenazim", family_samples:"NA24143", caller:"haplotypecaller"], file(params.ped, checkIfExists:true) ]) input[2] = [[],[]] diff --git a/tests/subworkflows/local/vcf_upd_updio/main.nf.test.snap b/tests/subworkflows/local/vcf_upd_updio/main.nf.test.snap index 330bb7e1..09731d58 100644 --- a/tests/subworkflows/local/vcf_upd_updio/main.nf.test.snap +++ b/tests/subworkflows/local/vcf_upd_updio/main.nf.test.snap @@ -6,7 +6,7 @@ { "id": "Ashkenazim", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "caller": "haplotypecaller", "child": "NA24385", "father": "NA24149", @@ -22,10 +22,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-27T13:36:54.518507627" + "timestamp": "2024-09-05T17:40:47.828005254" }, "default - sample": { "content": [ diff --git a/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test b/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test index f540a89c..6714fe38 100644 --- a/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test +++ b/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test @@ -31,14 +31,14 @@ nextflow_workflow { workflow { """ input[0] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:3], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385"], file(params.famvcf, checkIfExists:true), file(params.famtbi, checkIfExists:true), file(params.vcf1, checkIfExists:true), file(params.tbi1, checkIfExists:true) ]) input[1] = Channel.of([ - [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_count:3], + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143,NA24149,NA24385"], file(params.bed, checkIfExists:true), [] ]) diff --git a/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test.snap b/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test.snap index 3e0b9a14..7d04aca4 100644 --- a/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test.snap +++ b/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test.snap @@ -7,7 +7,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3 + "family_samples": "NA24143,NA24149,NA24385" }, "NA24143.tp.vcf.gz:md5,b28d3e84a6efa95bfbf673de310f62c1" ] @@ -18,7 +18,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3 + "family_samples": "NA24143,NA24149,NA24385" }, "NA24143.tp.vcf.gz.tbi:md5,8f8356fd93e093e9deb1c2c4c72cb65e" ] @@ -29,7 +29,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3 + "family_samples": "NA24143,NA24149,NA24385" }, "NA24143.fn.vcf.gz:md5,99830701ae0191110b706b20abe56857" ] @@ -40,7 +40,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3 + "family_samples": "NA24143,NA24149,NA24385" }, "NA24143.fn.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" ] @@ -51,7 +51,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3 + "family_samples": "NA24143,NA24149,NA24385" }, "NA24143.fp.vcf.gz:md5,2769bf65afefc821fe54a8b314b5d2be" ] @@ -62,7 +62,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3 + "family_samples": "NA24143,NA24149,NA24385" }, "NA24143.fp.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" ] @@ -73,7 +73,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3 + "family_samples": "NA24143,NA24149,NA24385" }, "NA24143.tp-baseline.vcf.gz:md5,6de63c7e2fa458ca88ea78c36f579056" ] @@ -84,7 +84,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3 + "family_samples": "NA24143,NA24149,NA24385" }, "NA24143.tp-baseline.vcf.gz.tbi:md5,8d399004d8c45fa795b70da32e23a6d5" ] @@ -95,7 +95,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3 + "family_samples": "NA24143,NA24149,NA24385" }, "NA24143.summary.txt:md5,11416903ca828b22bd64cf297f2db999" ] @@ -106,7 +106,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3 + "family_samples": "NA24143,NA24149,NA24385" }, "NA24143.phasing.txt:md5,38920536b8c3e241e873c07ba61762e6" ] @@ -117,7 +117,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3 + "family_samples": "NA24143,NA24149,NA24385" }, "NA24143.snp_roc.tsv.gz:md5,d29e7796d37dada43378e466af98c35a" ] @@ -128,7 +128,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3 + "family_samples": "NA24143,NA24149,NA24385" }, "NA24143.non_snp_roc.tsv.gz:md5,121b8b67d40efcaf1aad5064c6f3bfe9" ] @@ -139,7 +139,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3 + "family_samples": "NA24143,NA24149,NA24385" }, "NA24143.weighted_roc.tsv.gz:md5,f016f9a10e793836b9b53d702e591454" ] @@ -150,7 +150,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "roc_type": "snp" }, "NA24143.snp.png" @@ -162,7 +162,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "roc_type": "non_snp" }, "NA24143.non_snp.png" @@ -174,7 +174,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "roc_type": "weighted" }, "NA24143.weighted.png" @@ -186,7 +186,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "roc_type": "snp" }, "NA24143.snp.svg" @@ -198,7 +198,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "roc_type": "non_snp" }, "NA24143.non_snp.svg" @@ -210,7 +210,7 @@ "id": "NA24143", "sample": "NA24143", "family": "Ashkenazim", - "family_count": 3, + "family_samples": "NA24143,NA24149,NA24385", "roc_type": "weighted" }, "NA24143.weighted.svg" @@ -221,6 +221,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-04T17:19:41.712263383" + "timestamp": "2024-09-05T17:41:19.06545291" } } \ No newline at end of file From 0e99623ded289e2f498bdd25c7767268b473882f Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 20 Sep 2024 13:41:34 +0200 Subject: [PATCH 34/49] fix some small issues --- assets/samplesheet.csv | 2 +- main.nf | 6 +----- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index 2f8a87d7..b20e3926 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,4 +1,4 @@ sample,family,cram,crai,roi,ped,truth_vcf,truth_tbi,truth_bed,vardict_min_af NA24143,Proband_12345,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24143.cram,,,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/genome/test.ped,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24143.vcf.gz,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24143.vcf.gz.tbi,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/regions/roi.bed,0.01 NA24149,Proband_12345,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24149.cram,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24149.cram.crai,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/regions/roi.bed,,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24149.vcf.gz,,, -NA24149,Proband_12345,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24385.cram,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24385.cram.crai,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/regions/roi.bed,,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24385.vcf.gz,,, +NA24385,Proband_12345,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24385.cram,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/crams/NA24385.cram.crai,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/regions/roi.bed,,https://github.com/nf-cmgg/test-datasets/raw/germline/data/genomics/homo_sapiens/illumina/vcfs/NA24385.vcf.gz,,, diff --git a/main.nf b/main.nf index 0ca8b4c1..285e1280 100644 --- a/main.nf +++ b/main.nf @@ -177,7 +177,7 @@ workflow { } } - callers = params.callers.tokenize(",") + def callers = params.callers.tokenize(",") callers.each { caller -> if(!(caller in GlobalVariables.availableCallers)) { error("\"${caller}\" is not a supported callers please use one or more of these instead: ${GlobalVariables.availableCallers}")} } @@ -194,10 +194,6 @@ workflow { def multiqc_logo = params.multiqc_logo ?: "$projectDir/assets/CMGG_logo.png" -<<<<<<< HEAD - print(params.genomes) -======= ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 // // SUBWORKFLOW: Run initialisation tasks // From 6f687b9c052470af4acc7920b4cd9b223db386ac Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 20 Sep 2024 13:47:13 +0200 Subject: [PATCH 35/49] fix unresolved merge conflicts --- modules.json | 148 ------------------ .../bcftools/annotate/bcftools-annotate.diff | 16 -- .../nf-core/ensemblvep/vep/environment.yml | 3 - .../pedfilter/rtgtools-pedfilter.diff | 11 -- .../nf-core/samtools/faidx/environment.yml | 6 - .../somalier/relate/somalier-relate.diff | 11 -- modules/nf-core/tabix/tabix/environment.yml | 6 - modules/nf-core/untar/environment.yml | 6 - .../main.nf.test.snap | 16 -- .../local/vcf_annotation/main.nf.test.snap | 8 - .../main.nf.test.snap | 4 - 11 files changed, 235 deletions(-) diff --git a/modules.json b/modules.json index 8f6c09e3..19d1e586 100644 --- a/modules.json +++ b/modules.json @@ -7,84 +7,48 @@ "nf-core": { "bcftools/annotate": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "88ae68490e8f2478a1e1bbeedac970fd7cc73022", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"], "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff" }, "bcftools/concat": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/filter": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "bcftools/norm": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "f6cc00f107826cfaf1c933297b10ed1757b41479", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "bcftools/pluginscatter": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/query": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "34ac993e081b32d2170ab790d0386b74122f9d36", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "c32611ac6813055b9321d2827678e2f8aebcb394", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/stats": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "bedtools/intersect": { @@ -94,110 +58,62 @@ }, "bedtools/merge": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "a3d614e4a7b8691a259bcfe33ad80903217d6215", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "bedtools/split": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "6dc8a32e32158bb4d3f9af92c802233b5d4f8e4d", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "ensemblvep/download": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "gatk4/calibratedragstrmodel": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "3f42e07a1133064c569b0dbe182979527bca9e59", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "gatk4/composestrtablefile": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "926e2f394d01c71d3abbdbca9c588630bfe51abf", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "e6fe277739f5894711405af3e717b2470bd956b5", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "gatk4/genomicsdbimport": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "gatk4/genotypegvcfs": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "8b74c800af3d91e0d7bfbecb902308dc4369071c", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "gatk4/haplotypecaller": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "c332ea831f95f750be962c4b5de655f7a1e6e245", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "gawk": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "mosdepth": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "multiqc": { @@ -212,21 +128,13 @@ }, "rtgtools/pedfilter": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "c1c2a770cfb0bfbf093a2434a27f091ebbc65987", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"], "patch": "modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff" }, "rtgtools/rocplot": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "64770369d851c45c364e410e052ef9a6c3a7d2bb", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "rtgtools/vcfeval": { @@ -236,129 +144,73 @@ }, "samtools/convert": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "samtools/index": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "46eca555142d6e597729fcb682adcc791796f514", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "snpeff/snpeff": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "3ad7292d9b8da881386e9d5b58364d7da489b38b", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "somalier/extract": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "458c882987320e27fc90723ec96c127a243a5497", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "somalier/relate": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "458c882987320e27fc90723ec96c127a243a5497", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"], "patch": "modules/nf-core/somalier/relate/somalier-relate.diff" }, "tabix/bgzip": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "b20be35facfc5acdc1259f132ed79339d79e989f", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "tabix/tabix": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff"] }, "untar": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "vardictjava": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "e61e5a13ef49c5595986bd31efb85c3f0709a282", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "vcf2db": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] }, "vcfanno": { "branch": "master", -<<<<<<< HEAD - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", -======= "git_sha": "9a8bba5910982ae637dedb8664e3121db77e173f", ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 "installed_by": ["modules"] } } diff --git a/modules/nf-core/bcftools/annotate/bcftools-annotate.diff b/modules/nf-core/bcftools/annotate/bcftools-annotate.diff index e284f014..518cee56 100644 --- a/modules/nf-core/bcftools/annotate/bcftools-annotate.diff +++ b/modules/nf-core/bcftools/annotate/bcftools-annotate.diff @@ -1,9 +1,4 @@ Changes in module 'nf-core/bcftools/annotate' -<<<<<<< HEAD -'modules/nf-core/bcftools/annotate/environment.yml' is unchanged -'modules/nf-core/bcftools/annotate/meta.yml' is unchanged -======= ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 Changes in 'bcftools/annotate/main.nf': --- modules/nf-core/bcftools/annotate/main.nf +++ modules/nf-core/bcftools/annotate/main.nf @@ -18,16 +13,6 @@ Changes in 'bcftools/annotate/main.nf': output: tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf -<<<<<<< HEAD -'modules/nf-core/bcftools/annotate/tests/main.nf.test.snap' is unchanged -'modules/nf-core/bcftools/annotate/tests/tags.yml' is unchanged -'modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config' is unchanged -'modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config' is unchanged -'modules/nf-core/bcftools/annotate/tests/vcf.config' is unchanged -'modules/nf-core/bcftools/annotate/tests/main.nf.test' is unchanged -'modules/nf-core/bcftools/annotate/tests/bcf.config' is unchanged -'modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config' is unchanged -======= 'modules/nf-core/bcftools/annotate/environment.yml' is unchanged 'modules/nf-core/bcftools/annotate/meta.yml' is unchanged 'modules/nf-core/bcftools/annotate/tests/tags.yml' is unchanged @@ -38,5 +23,4 @@ Changes in 'bcftools/annotate/main.nf': 'modules/nf-core/bcftools/annotate/tests/bcf.config' is unchanged 'modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config' is unchanged 'modules/nf-core/bcftools/annotate/tests/main.nf.test.snap' is unchanged ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 ************************************************************ diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml index 5fe0afb1..87b88372 100644 --- a/modules/nf-core/ensemblvep/vep/environment.yml +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -1,7 +1,4 @@ -<<<<<<< HEAD -======= name: ensemblvep_vep ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 channels: - conda-forge - bioconda diff --git a/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff b/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff index a8ca8d7a..18590bf8 100644 --- a/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff +++ b/modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff @@ -1,9 +1,4 @@ Changes in module 'nf-core/rtgtools/pedfilter' -<<<<<<< HEAD -'modules/nf-core/rtgtools/pedfilter/environment.yml' is unchanged -'modules/nf-core/rtgtools/pedfilter/meta.yml' is unchanged -======= ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 Changes in 'rtgtools/pedfilter/main.nf': --- modules/nf-core/rtgtools/pedfilter/main.nf +++ modules/nf-core/rtgtools/pedfilter/main.nf @@ -16,15 +11,9 @@ Changes in 'rtgtools/pedfilter/main.nf': -<<<<<<< HEAD -'modules/nf-core/rtgtools/pedfilter/tests/main.nf.test.snap' is unchanged -'modules/nf-core/rtgtools/pedfilter/tests/nextflow.config' is unchanged -'modules/nf-core/rtgtools/pedfilter/tests/main.nf.test' is unchanged -======= 'modules/nf-core/rtgtools/pedfilter/environment.yml' is unchanged 'modules/nf-core/rtgtools/pedfilter/meta.yml' is unchanged 'modules/nf-core/rtgtools/pedfilter/tests/main.nf.test' is unchanged 'modules/nf-core/rtgtools/pedfilter/tests/main.nf.test.snap' is unchanged 'modules/nf-core/rtgtools/pedfilter/tests/nextflow.config' is unchanged ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 ************************************************************ diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index 37884bae..f8450fa5 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -1,15 +1,9 @@ -<<<<<<< HEAD -channels: - - conda-forge - - bioconda -======= name: samtools_faidx channels: - conda-forge - bioconda - defaults ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 dependencies: - bioconda::htslib=1.20 diff --git a/modules/nf-core/somalier/relate/somalier-relate.diff b/modules/nf-core/somalier/relate/somalier-relate.diff index 513bc3ec..918d80b2 100644 --- a/modules/nf-core/somalier/relate/somalier-relate.diff +++ b/modules/nf-core/somalier/relate/somalier-relate.diff @@ -1,9 +1,4 @@ Changes in module 'nf-core/somalier/relate' -<<<<<<< HEAD -'modules/nf-core/somalier/relate/environment.yml' is unchanged -'modules/nf-core/somalier/relate/meta.yml' is unchanged -======= ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 Changes in 'somalier/relate/main.nf': --- modules/nf-core/somalier/relate/main.nf +++ modules/nf-core/somalier/relate/main.nf @@ -33,15 +28,9 @@ Changes in 'somalier/relate/main.nf': cat <<-END_VERSIONS > versions.yml "${task.process}": -<<<<<<< HEAD -'modules/nf-core/somalier/relate/tests/main.nf.test.snap' is unchanged -'modules/nf-core/somalier/relate/tests/tags.yml' is unchanged -'modules/nf-core/somalier/relate/tests/main.nf.test' is unchanged -======= 'modules/nf-core/somalier/relate/environment.yml' is unchanged 'modules/nf-core/somalier/relate/meta.yml' is unchanged 'modules/nf-core/somalier/relate/tests/tags.yml' is unchanged 'modules/nf-core/somalier/relate/tests/main.nf.test' is unchanged 'modules/nf-core/somalier/relate/tests/main.nf.test.snap' is unchanged ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 ************************************************************ diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index 8fd6ad50..4d1f9dd4 100644 --- a/modules/nf-core/tabix/tabix/environment.yml +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -1,15 +1,9 @@ -<<<<<<< HEAD -channels: - - conda-forge - - bioconda -======= name: tabix_tabix channels: - conda-forge - bioconda - defaults ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 dependencies: - bioconda::htslib=1.20 diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 58e0ef80..4f498244 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,14 +1,8 @@ -<<<<<<< HEAD -channels: - - conda-forge - - bioconda -======= name: untar channels: - conda-forge - bioconda - defaults ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 dependencies: - conda-forge::grep=3.11 - conda-forge::sed=4.8 diff --git a/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap b/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap index 719e14c1..a0aec425 100644 --- a/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap +++ b/tests/subworkflows/local/cram_call_genotype_gatk4/main.nf.test.snap @@ -40,11 +40,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, -<<<<<<< HEAD - "timestamp": "2024-09-05T11:18:02.353352239" -======= "timestamp": "2024-09-05T17:35:02.44674969" ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 }, "filter - family": { "content": [ @@ -70,11 +66,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, -<<<<<<< HEAD - "timestamp": "2024-09-05T11:19:14.883570897" -======= "timestamp": "2024-09-05T17:35:46.768542501" ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 }, "default - gvcfs": { "content": [ @@ -124,11 +116,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, -<<<<<<< HEAD - "timestamp": "2024-09-05T11:16:25.448441115" -======= "timestamp": "2024-09-05T17:33:52.045772718" ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 }, "only_call - family": { "content": [ @@ -171,10 +159,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, -<<<<<<< HEAD - "timestamp": "2024-09-05T11:21:57.601081087" -======= "timestamp": "2024-09-06T14:26:29.249708339" ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 } } \ No newline at end of file diff --git a/tests/subworkflows/local/vcf_annotation/main.nf.test.snap b/tests/subworkflows/local/vcf_annotation/main.nf.test.snap index f9e7b1ad..d3ebc487 100644 --- a/tests/subworkflows/local/vcf_annotation/main.nf.test.snap +++ b/tests/subworkflows/local/vcf_annotation/main.nf.test.snap @@ -22,11 +22,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, -<<<<<<< HEAD - "timestamp": "2024-09-05T12:53:05.739638954" -======= "timestamp": "2024-09-05T17:39:23.107888975" ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 }, "vcfanno": { "content": [ @@ -51,10 +47,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, -<<<<<<< HEAD - "timestamp": "2024-09-05T12:53:27.894947052" -======= "timestamp": "2024-09-05T17:39:39.640344999" ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 } } \ No newline at end of file diff --git a/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test.snap b/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test.snap index 41c882d3..7d04aca4 100644 --- a/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test.snap +++ b/tests/subworkflows/local/vcf_validate_small_variants/main.nf.test.snap @@ -221,10 +221,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, -<<<<<<< HEAD - "timestamp": "2024-09-04T17:19:41.712263383" -======= "timestamp": "2024-09-05T17:41:19.06545291" ->>>>>>> 3726a041a4fa98d73748421c2a5e8a5b3cd6e7c1 } } \ No newline at end of file From bb46fe2c5de29dc9ae8a3972ff4c7fbafb9f1376 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 20 Sep 2024 13:49:20 +0200 Subject: [PATCH 36/49] make pre-commit happy --- subworkflows/local/watchpath_handling/main.nf | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/watchpath_handling/main.nf b/subworkflows/local/watchpath_handling/main.nf index 88cf3fbc..eca869b1 100644 --- a/subworkflows/local/watchpath_handling/main.nf +++ b/subworkflows/local/watchpath_handling/main.nf @@ -21,7 +21,7 @@ workflow WATCHPATH_HANDLING { def expected_files = [done_file.name] // Initialize samplesheet to keep the linter happy - ch_samplesheet_watched = Channel.empty() + def ch_samplesheet_watched = Channel.empty() // Pedigree handling def pedigree = new Pedigree(pedFile) @@ -40,7 +40,7 @@ workflow WATCHPATH_HANDLING { // Watchpath logic def is_watch = false row = row.collect { input -> - input_name = input instanceof Path ? input.name : input as String + def input_name = input instanceof Path ? input.name : input as String if (input_name.startsWith("watch:")) { is_watch = true expected_files.add(input_name.replace("watch:", "")) @@ -102,7 +102,7 @@ workflow WATCHPATH_HANDLING { if (watchdir && expected_files.size() > 1) { - watchdir_path = file(watchdir) + def watchdir_path = file(watchdir) if (!watchdir_path.exists()) { // Create the watchdir if it doesn't exist (this is a failsafe) watchdir_path.mkdir() @@ -151,7 +151,6 @@ workflow WATCHPATH_HANDLING { } else { ch_samplesheet_watched = ch_samplesheet_all - } ch_samplesheet_watched From 963f6b59eece4290d9fd47a361f3856a0a58e6ba Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 20 Sep 2024 14:06:33 +0200 Subject: [PATCH 37/49] [no-cancel] fix nf-core lint --- .github/workflows/ci.yml | 2 +- nextflow.config | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 37ebe5ce..f5513eae 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -13,7 +13,7 @@ env: concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" - cancel-in-progress: true + cancel-in-progress: "${{ !contains(github.event.head_commit.message, '[no-cancel]') }}" jobs: test_all: diff --git a/nextflow.config b/nextflow.config index 46e627fa..8a80581b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,6 +12,7 @@ params { // Input options input = null ped = null + watchdir = null // Pipeline specific parameters scatter_count = 40 From 4efe0e361fbff50a2a1cdb98b8c3f93a01bf561b Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 20 Sep 2024 14:13:42 +0200 Subject: [PATCH 38/49] [no-cancel] fix nf-core lint --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f5513eae..26383305 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -13,7 +13,7 @@ env: concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" - cancel-in-progress: "${{ !contains(github.event.head_commit.message, '[no-cancel]') }}" + cancel-in-progress: "${{ contains(github.event.head_commit.message, '[no-cancel]') }}" jobs: test_all: From 773eeafb1e05ca39d11bbbdeb616c82c27fbfd0a Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 23 Sep 2024 12:35:44 +0200 Subject: [PATCH 39/49] fix prepare tests --- .../cram_prepare_samtools_bedtools/main.nf.test | 3 +++ .../main.nf.test.snap | 13 +++++++++++-- 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test b/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test index 472a1eae..0a69a066 100644 --- a/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test +++ b/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test @@ -145,6 +145,9 @@ nextflow_workflow { input[1] = Channel.of([ [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", duplicate_count:2], file(params.bed, checkIfExists:true) + ],[ + [id:"NA24143", sample:"NA24143", family:"Ashkenazim", family_samples:"NA24143", duplicate_count:2], + [] ]) input[2] = Channel.value([ [id:"fasta"], diff --git a/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test.snap b/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test.snap index 47b214c1..e4ad6291 100644 --- a/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test.snap +++ b/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test.snap @@ -15,7 +15,16 @@ ] ], [ - + [ + { + "id": "NA24143", + "sample": "NA24143", + "family": "Ashkenazim", + "family_samples": "NA24143", + "duplicate_count": 2 + }, + "NA24143_intersect.bed:md5,b87069698afefb15282d069e56110046" + ] ], [ @@ -25,7 +34,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-06T14:40:18.974586888" + "timestamp": "2024-09-23T11:46:20.577603661" }, "default - WGS": { "content": [ From c9c4134c0dd2060f26f4feb76a55bd7daa5c6bbe Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 23 Sep 2024 12:36:10 +0200 Subject: [PATCH 40/49] undo no cancel --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 26383305..37ebe5ce 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -13,7 +13,7 @@ env: concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" - cancel-in-progress: "${{ contains(github.event.head_commit.message, '[no-cancel]') }}" + cancel-in-progress: true jobs: test_all: From 3c5cf09f525cbf6c463113c0d9d7b9b07c3c1ca7 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 23 Sep 2024 12:45:44 +0200 Subject: [PATCH 41/49] fix snapshots --- tests/pipeline/callers/main.nf.test.snap | 6 +++--- tests/pipeline/default/main.nf.test.snap | 2 +- tests/pipeline/gvcfs/main.nf.test.snap | 2 +- tests/pipeline/variations/main.nf.test.snap | 12 ++++++------ tests/pipeline/variations2/main.nf.test.snap | 10 +++++----- 5 files changed, 16 insertions(+), 16 deletions(-) diff --git a/tests/pipeline/callers/main.nf.test.snap b/tests/pipeline/callers/main.nf.test.snap index babe4775..f5629747 100644 --- a/tests/pipeline/callers/main.nf.test.snap +++ b/tests/pipeline/callers/main.nf.test.snap @@ -2,7 +2,7 @@ "haplotypecaller": { "content": [ [ - "[:]" + ], [ "NA24143/NA24143.bed", @@ -47,7 +47,7 @@ "vardict + haplotypecaller": { "content": [ [ - "[:]" + ], [ "NA24143/NA24143.bed", @@ -110,7 +110,7 @@ "vardict": { "content": [ [ - "[:]" + ], [ "NA24143/NA24143.bed", diff --git a/tests/pipeline/default/main.nf.test.snap b/tests/pipeline/default/main.nf.test.snap index 30d78cd0..ab43dc3b 100644 --- a/tests/pipeline/default/main.nf.test.snap +++ b/tests/pipeline/default/main.nf.test.snap @@ -2,7 +2,7 @@ "default": { "content": [ [ - "[:]" + ], [ "NA24143/NA24143.bed", diff --git a/tests/pipeline/gvcfs/main.nf.test.snap b/tests/pipeline/gvcfs/main.nf.test.snap index 03a3b401..3b3b89d8 100644 --- a/tests/pipeline/gvcfs/main.nf.test.snap +++ b/tests/pipeline/gvcfs/main.nf.test.snap @@ -2,7 +2,7 @@ "gvcfs": { "content": [ [ - "[:]" + ], [ "multiqc/multiqc_plots", diff --git a/tests/pipeline/variations/main.nf.test.snap b/tests/pipeline/variations/main.nf.test.snap index ee31f079..348a2942 100644 --- a/tests/pipeline/variations/main.nf.test.snap +++ b/tests/pipeline/variations/main.nf.test.snap @@ -2,7 +2,7 @@ "filter": { "content": [ [ - "[:]" + ], [ "NA24143/NA24143.bed", @@ -47,7 +47,7 @@ "only_call": { "content": [ [ - "[:]" + ], [ "NA24143/NA24143.bed", @@ -85,7 +85,7 @@ "annotate + vcfanno": { "content": [ [ - "[:]" + ], [ "NA24143/NA24143.bed", @@ -131,7 +131,7 @@ "automap": { "content": [ [ - "[:]" + ], [ "NA24143/NA24143.bed", @@ -188,7 +188,7 @@ "only_merge": { "content": [ [ - "[:]" + ], [ "NA24143/NA24143.bed", @@ -227,7 +227,7 @@ "annotate": { "content": [ [ - "[:]" + ], [ "NA24143/NA24143.bed", diff --git a/tests/pipeline/variations2/main.nf.test.snap b/tests/pipeline/variations2/main.nf.test.snap index ba145d7e..053dd3eb 100644 --- a/tests/pipeline/variations2/main.nf.test.snap +++ b/tests/pipeline/variations2/main.nf.test.snap @@ -2,7 +2,7 @@ "gemini": { "content": [ [ - "[:]" + ], [ "NA24143/NA24143.bed", @@ -48,7 +48,7 @@ "normalize": { "content": [ [ - "[:]" + ], [ "NA24143/NA24143.bed", @@ -93,7 +93,7 @@ "updio": { "content": [ [ - "[:]" + ], [ "NA24143/NA24143.bed", @@ -138,7 +138,7 @@ "add_ped": { "content": [ [ - "[:]" + ], [ "NA24143/NA24143.bed", @@ -183,7 +183,7 @@ "validate": { "content": [ [ - "[:]" + ], [ "NA24143/NA24143.bed", From 56ba4a1be1324c0acfbacb8f591c6e2692a459fb Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 23 Sep 2024 13:10:29 +0200 Subject: [PATCH 42/49] make genomes ignore true --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 8a80581b..bc52e3ff 100644 --- a/nextflow.config +++ b/nextflow.config @@ -82,7 +82,7 @@ params { igenomes_ignore = false genome = "GRCh38" genomes_base = "/references/" - genomes_ignore = false + genomes_ignore = true // Boilerplate options outdir = null From 070a9cbefc1acbb22738bdcd2d89ae821efdcc78 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 23 Sep 2024 13:50:31 +0200 Subject: [PATCH 43/49] fix an issue with the validation workflow --- .../local/vcf_validate_small_variants/main.nf | 32 ------------------- workflows/germline.nf | 21 ++++-------- 2 files changed, 7 insertions(+), 46 deletions(-) diff --git a/subworkflows/local/vcf_validate_small_variants/main.nf b/subworkflows/local/vcf_validate_small_variants/main.nf index eaa17579..63ca83fd 100644 --- a/subworkflows/local/vcf_validate_small_variants/main.nf +++ b/subworkflows/local/vcf_validate_small_variants/main.nf @@ -14,38 +14,6 @@ workflow VCF_VALIDATE_SMALL_VARIANTS { ch_versions = Channel.empty() - happy_vcf = Channel.empty() - happy_tbi = Channel.empty() - happy_indel_roc = Channel.empty() - happy_indel_roc_pass = Channel.empty() - happy_snp_roc = Channel.empty() - happy_snp_roc_pass = Channel.empty() - happy_roc = Channel.empty() - happy_summary = Channel.empty() - happy_extended_csv = Channel.empty() - - vcfeval_true_positive_vcf = Channel.empty() - vcfeval_true_positive_vcf_tbi = Channel.empty() - vcfeval_false_negative_vcf = Channel.empty() - vcfeval_false_negative_vcf_tbi = Channel.empty() - vcfeval_false_positive_vcf = Channel.empty() - vcfeval_false_positive_vcf_tbi = Channel.empty() - vcfeval_true_positive_baseline_vcf = Channel.empty() - vcfeval_true_positive_baseline_vcf_tbi = Channel.empty() - vcfeval_summary = Channel.empty() - vcfeval_phasing = Channel.empty() - vcfeval_snp_roc = Channel.empty() - vcfeval_non_snp_roc = Channel.empty() - vcfeval_weighted_roc = Channel.empty() - - rtgtools_snp_png_rocplot = Channel.empty() - rtgtools_non_snp_png_rocplot = Channel.empty() - rtgtools_weighted_png_rocplot = Channel.empty() - - rtgtools_snp_svg_rocplot = Channel.empty() - rtgtools_non_snp_svg_rocplot = Channel.empty() - rtgtools_weighted_svg_rocplot = Channel.empty() - ch_input = ch_vcf.join(ch_beds, failOnDuplicate: true, failOnMismatch: true) RTGTOOLS_VCFEVAL( diff --git a/workflows/germline.nf b/workflows/germline.nf index ec5987a7..fe3e04b6 100644 --- a/workflows/germline.nf +++ b/workflows/germline.nf @@ -342,12 +342,9 @@ workflow GERMLINE { gvcf: [new_meta, gvcf, tbi] // Optional channel containing the GVCFs and their optional indices cram: [new_meta, cram, crai] // Mandatory channel containing the CRAM files and their optional indices roi: [new_meta, roi_file] // Optional channel containing the ROI BED files for WES samples - family_samples: [meta.family, meta.family_samples.tokenize(",")] // A channel containing the samples per family } .set { ch_input } - ch_family_samples = ch_input.family_samples.distinct() - // // Create the GVCF index if it's missing // @@ -595,14 +592,15 @@ workflow GERMLINE { ch_input.truth_variants .map { meta, vcf, tbi, bed -> - [ groupKey(meta, meta.duplicate_count), vcf, tbi, bed ] + def new_meta = meta - meta.subMap("duplicate_count") + [ groupKey(new_meta, meta.duplicate_count), vcf, tbi, bed ] } .groupTuple() .map { meta, vcf, tbi, bed -> // Get only one VCF for samples that were given multiple times - one_vcf = vcf.find { vcf_file -> vcf_file != [] } ?: [] - one_tbi = tbi.find { tbi_file -> tbi_file != [] } ?: [] - one_bed = bed.find { bed_file -> bed_file != [] } ?: [] + def one_vcf = vcf.find { vcf_file -> vcf_file != [] } ?: [] + def one_tbi = tbi.find { tbi_file -> tbi_file != [] } ?: [] + def one_bed = bed.find { bed_file -> bed_file != [] } ?: [] [ meta, one_vcf, one_tbi, one_bed ] } .branch { meta, vcf, tbi, bed -> @@ -637,12 +635,7 @@ workflow GERMLINE { ch_final_vcfs .map { meta, vcf, tbi -> def new_meta = meta - meta.subMap("family_samples") - [ meta.family, new_meta, vcf, tbi ] - } - .combine(ch_family_samples, by:0) - .map { family, meta, vcf, tbi, samples -> - def sample = meta.sample ? [meta.sample] : samples - [ meta, vcf, tbi, sample ] + [ new_meta, vcf, tbi, meta.family_samples.tokenize(",") ] } .transpose(by: 3) .map { meta, vcf, tbi, sample -> @@ -654,7 +647,7 @@ workflow GERMLINE { ] [ new_meta, vcf, tbi ] } - .combine(ch_truths, by:0) + .join(ch_truths, failOnMismatch:true, failOnDuplicate:true) .filter { meta, vcf, tbi, truth_vcf, truth_tbi, truth_bed -> // Filter out all samples that have no truth VCF truth_vcf != [] From fd15c142119ba054ea8b00bb361c6302bfab3ef7 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 23 Sep 2024 14:45:18 +0200 Subject: [PATCH 44/49] also filter out low coverage regions --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index f07bb4f2..7c54ceb0 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -101,7 +101,7 @@ process { withName: "^.*CRAM_PREPARE_SAMTOOLS_BEDTOOLS:FILTER_BEDS\$" { ext.prefix = { "${meta.id}.filter"} - ext.args = "-vE \"NO_COVERAGE${params.keep_alt_contigs ? "" : "|alt|random|decoy|Un"}\"" + ext.args = "-vE \"LOW_COVERAGE|NO_COVERAGE${params.keep_alt_contigs ? "" : "|alt|random|decoy|Un"}\"" ext.args2 = "-d 150" publishDir = [ overwrite: true, From 9ac108fde5da024871eb7892b76a1a40f84d842c Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 23 Sep 2024 14:47:57 +0200 Subject: [PATCH 45/49] update changelog --- CHANGELOG.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 50d6471f..d35df382 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,11 +5,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v1.8.0dev +## New features + +1. Added `watchpath` functionality to the pipeline. Add the `watch:` prefix to a file basename in the samplesheet and the pipeline will automatically wait for the file to be created in the `--watchdir` directory (the lookup happens recursively) + ## Changes 1. Bumped the minimal support nextflow version to `24.04.0` 2. Bumped all modules to the newest versions 3. The pipeline now also outputs `csi` indices +4. Low coverage regions (regions with less than 5 reads) are no longer considered for variant calling ## Refactors From df9ecc380f6f3f768a2226bfc2d0f4dda5955465 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 23 Sep 2024 14:57:24 +0200 Subject: [PATCH 46/49] fix snap --- .../local/cram_prepare_samtools_bedtools/main.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test.snap b/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test.snap index e4ad6291..cbd7535e 100644 --- a/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test.snap +++ b/tests/subworkflows/local/cram_prepare_samtools_bedtools/main.nf.test.snap @@ -60,7 +60,7 @@ "family_samples": "NA24143", "duplicate_count": 1 }, - "NA24143.filter.bed:md5,9fc0cc2e4403678f18bc8b18646abd66" + "NA24143.filter.bed:md5,85a5568a6976ed455caa712991b30ac2" ] ], [ @@ -71,7 +71,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-06T14:32:19.290286542" + "timestamp": "2024-09-23T14:56:11.141634788" }, "default - WES": { "content": [ From 231059ad41e75db44a28eedbb8f3f704ec571c1b Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 23 Sep 2024 16:09:44 +0200 Subject: [PATCH 47/49] rename master branch to main --- .github/CONTRIBUTING.md | 4 ++-- .github/PULL_REQUEST_TEMPLATE.md | 4 ++-- .github/workflows/branch.yml | 16 ++++++++-------- .github/workflows/build-docs.yml | 1 - .github/workflows/download_pipeline.yml | 6 +++--- CHANGELOG.md | 1 + 6 files changed, 16 insertions(+), 16 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index fb0acc75..69065bdb 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -52,9 +52,9 @@ These tests are run both with the latest available version of `Nextflow` and als :warning: Only in the unlikely and regretful event of a release happening with a bug. -- On your own fork, make a new branch `patch` based on `upstream/master`. +- On your own fork, make a new branch `patch` based on `upstream/main`. - Fix the bug, and bump version (X.Y.Z+1). -- A PR should be made on `master` from patch to directly this particular bug. +- A PR should be made on `main` from patch to directly this particular bug. ## Pipeline contribution conventions diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 245df89f..b8950db4 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs). Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. -Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-cmgg/germline/tree/master/.github/CONTRIBUTING.md) +Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-cmgg/germline/tree/main/.github/CONTRIBUTING.md) --> ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-cmgg/germline/tree/master/.github/CONTRIBUTING.md) +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-cmgg/germline/tree/main/.github/CONTRIBUTING.md) - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 5d7a55fc..4cad70ae 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -1,15 +1,15 @@ name: nf-core branch protection -# This workflow is triggered on PRs to master branch on the repository -# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` +# This workflow is triggered on PRs to main branch on the repository +# It fails when someone tries to make a PR against the nf-core `main` branch instead of `dev` on: pull_request_target: - branches: [master] + branches: [main] jobs: test: runs-on: ubuntu-latest steps: - # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches + # PRs to the nf-core repo main branch are only ok if coming from the nf-core repo `dev` or any `patch` branches - name: Check PRs if: github.repository == 'nf-cmgg/germline' run: | @@ -22,7 +22,7 @@ jobs: uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 with: message: | - ## This PR is against the `master` branch :x: + ## This PR is against the `main` branch :x: * Do not close this PR * Click _Edit_ and change the `base` to `dev` @@ -32,9 +32,9 @@ jobs: Hi @${{ github.event.pull_request.user.login }}, - It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch. - The `master` branch on nf-core repositories should always contain code from the latest release. - Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. + It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `main` branch. + The `main` branch on nf-core repositories should always contain code from the latest release. + Because of this, PRs to `main` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit. diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml index a7eded4d..be1ba144 100644 --- a/.github/workflows/build-docs.yml +++ b/.github/workflows/build-docs.yml @@ -2,7 +2,6 @@ name: build docs on: push: branches: - - master - main - dev permissions: diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 2d20d644..4a2e3eb4 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core download' # Run the workflow when: # - dispatched manually -# - when a PR is opened or reopened to master branch +# - when a PR is opened or reopened to main branch # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. on: workflow_dispatch: @@ -17,10 +17,10 @@ on: - edited - synchronize branches: - - master + - main pull_request_target: branches: - - master + - main env: NXF_ANSI_LOG: false diff --git a/CHANGELOG.md b/CHANGELOG.md index 50d6471f..acb92b97 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 1. Bumped the minimal support nextflow version to `24.04.0` 2. Bumped all modules to the newest versions 3. The pipeline now also outputs `csi` indices +4. Rename the `master` branch to `main` ## Refactors From f6ac2f7b873c28c1a27448c9458e25f8f14a67aa Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 23 Sep 2024 16:18:15 +0200 Subject: [PATCH 48/49] fix nf-core lint --- .nf-core.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.nf-core.yml b/.nf-core.yml index d6b21f91..7b994ce9 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -11,6 +11,7 @@ lint: files_unchanged: - ".github/CONTRIBUTING.md" - ".github/PULL_REQUEST_TEMPLATE.md" + - ".github/workflows/branch.yml" - ".github/workflows/linting_comment.yml" - ".github/workflows/linting.yml" - "CODE_OF_CONDUCT.md" From 2556e9c9e2a74addb28163eb61691d669cbca2d5 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 23 Sep 2024 16:32:28 +0200 Subject: [PATCH 49/49] update version --- CHANGELOG.md | 2 +- nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 73eb840c..517ea82d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.8.0dev +## v1.8.0 - Optimistic Oostkamp - [September 23 2024] ## New features diff --git a/nextflow.config b/nextflow.config index bc52e3ff..4346d485 100644 --- a/nextflow.config +++ b/nextflow.config @@ -295,7 +295,7 @@ manifest { description = """A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.0' - version = '1.8.0dev' + version = '1.8.0' doi = '' }