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improve schema for references
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@maxulysse
maxulysse committed Jan 27, 2025
1 parent 09721e7 commit a42f84d
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Showing 5 changed files with 252 additions and 361 deletions.
3 changes: 1 addition & 2 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,6 @@ include { ANNOTATION_CACHE_INITIALISATION } from './subworkflows/local/annotatio
include { DOWNLOAD_CACHE_SNPEFF_VEP } from './subworkflows/local/download_cache_snpeff_vep'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_sarek_pipeline'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_sarek_pipeline'
include { PREPARE_GENOME } from './subworkflows/local/prepare_genome'
include { PREPARE_INTERVALS } from './subworkflows/local/prepare_intervals'
include { PREPARE_REFERENCE_CNVKIT } from './subworkflows/local/prepare_reference_cnvkit'
/*
Expand All @@ -44,11 +43,11 @@ workflow {
PIPELINE_INITIALISATION(
params.version,
params.validate_params,
params.monochrome_logs,
args,
params.outdir,
params.input,
params.references,
params.step,
)

// WORKFLOW: Run main workflow
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92 changes: 63 additions & 29 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,9 @@ params {

// Mandatory arguments
// Input options
input = null // No default input
input_restart = null // No default automatic input
step = 'mapping' // Starts with mapping
input = null // No default input
input_restart = null // No default automatic input
step = 'mapping' // Starts with mapping

// References
genome = 'GATK/GRCh38'
Expand All @@ -22,9 +22,44 @@ params {
references = "${params.references_config_base}/igenomes/${genome}.yml"
snpeff_cache = 's3://annotation-cache/snpeff_cache/'
vep_cache = 's3://annotation-cache/vep_cache/'
build_only_index = false // Only build the reference indexes
download_cache = false // Do not download annotation cache

// params for references in yaml file
ascat_alleles = null
ascat_genome = null
ascat_loci = null
ascat_loci_gc = null
ascat_loci_rt = null
bwa = null
bwamem2 = null
cf_chrom_len = null
chr_dir = null
dbsnp = null
dbsnp_tbi = null
dbsnp_vqsr = null
dict = null
dragmap = null
fasta = null
fasta_fai = null
germline_resource = null
germline_resource_tbi = null
intervals = null
known_indels = null
known_indels_tbi = null
known_indels_vqsr = null
known_snps = null
known_snps_tbi = null
known_snps_vqsr = null
mappability = null
ngscheckmate_bed = null
pon = null
pon_tbi = null
sentieon_dnascope_model = null
snpeff_db = null
vep_cache_version = null
vep_genome = null
vep_species = null

// Main options
no_intervals = false // Intervals will be built from the fasta file
nucleotides_per_second = 200000 // Default interval size
Expand Down Expand Up @@ -80,32 +115,32 @@ params {
wes = false // Set to true, if data is exome/targeted sequencing data. Used to use correct models in various variant callers

// Annotation
bcftools_annotations = null // No extra annotation file
bcftools_annotations_tbi = null // No extra annotation file index
bcftools_header_lines = null // No header lines to be added to the VCF file
dbnsfp = null // No dbnsfp processed file
dbnsfp_consequence = null // No default consequence for dbnsfp plugin
dbnsfp_fields = "rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF" // Default fields for dbnsfp plugin
dbnsfp_tbi = null // No dbnsfp processed file index
outdir_cache = null // No default outdir cache
spliceai_indel = null // No spliceai_indel file
spliceai_indel_tbi = null // No spliceai_indel file index
spliceai_snv = null // No spliceai_snv file
spliceai_snv_tbi = null // No spliceai_snv file index
vep_custom_args = "--everything --filter_common --per_gene --total_length --offline --format vcf" // Default arguments for VEP
vep_dbnsfp = null // dbnsfp plugin disabled within VEP
vep_include_fasta = false // Don't use fasta file for annotation with VEP
vep_loftee = null // loftee plugin disabled within VEP
vep_out_format = "vcf"
vep_spliceai = null // spliceai plugin disabled within VEP
vep_spliceregion = null // spliceregion plugin disabled within VEP
vep_version = "111.0-0" // Should be updated when we update VEP, needs this to get full path to some plugins
bcftools_annotations = null // No extra annotation file
bcftools_annotations_tbi = null // No extra annotation file index
bcftools_header_lines = null // No header lines to be added to the VCF file
dbnsfp = null // No dbnsfp processed file
dbnsfp_consequence = null // No default consequence for dbnsfp plugin
dbnsfp_fields = "rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF" // Default fields for dbnsfp plugin
dbnsfp_tbi = null // No dbnsfp processed file index
outdir_cache = null // No default outdir cache
spliceai_indel = null // No spliceai_indel file
spliceai_indel_tbi = null // No spliceai_indel file index
spliceai_snv = null // No spliceai_snv file
spliceai_snv_tbi = null // No spliceai_snv file index
vep_custom_args = "--everything --filter_common --per_gene --total_length --offline --format vcf" // Default arguments for VEP
vep_dbnsfp = null // dbnsfp plugin disabled within VEP
vep_include_fasta = false // Don't use fasta file for annotation with VEP
vep_loftee = null // loftee plugin disabled within VEP
vep_out_format = "vcf"
vep_spliceai = null // spliceai plugin disabled within VEP
vep_spliceregion = null // spliceregion plugin disabled within VEP
vep_version = "111.0-0" // Should be updated when we update VEP, needs this to get full path to some plugins

// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null

// Boilerplate options
Expand Down Expand Up @@ -389,7 +424,6 @@ plugins {
}

validation {
defaultIgnoreParams = ["genomes"]
lenientMode = true
help {
enabled = true
Expand Down
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