Prevent Pyrodigal from adding stop codon indicators

[jasmezz]

This introduces a new param which prevents Pyrodigal from appending * to coding sequences which contain a stop codon. It has been reported in #373 that AMPlify ignores sequences containing non-sequence characters like *, thus this Pyrodigal flag should be used.

The other annotation tools don't have such a flag unfortunately. We could think about adding a filtering step before AMPlify execution if the AMPlify authors don't solve this upstream (see issue bcgsc/AMPlify#17).

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
• If necessary, also make a PR on the nf-core/funcscan branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d34dbf0

+| ✅ 344 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  13 tests had warnings |!

❗ Test warnings:

• files_exist - File not found: conf/igenomes.config
• files_exist - File not found: conf/igenomes_ignored.config
• pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

  \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-funcscan_logo_dark.png">\n <img alt="nf-core/funcscan" src="docs/images/nf-core-funcscan_logo_light.png">\n \n

  \n\n\n\n\n\n\n\n\n\n\n\n\n\n## Introduction\n\nnf-core/funcscan is a bioinformatics pipeline that ...\n\n TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n\n\n Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. \n Fill in short bullet-pointed list of the default steps in the pipeline 2. Present QC for raw reads (MultiQC)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.\n\n Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\nsamplesheet.csv:\n\ncsv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n\n\nNow, you can run the pipeline using:\n\n update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run nf-core/funcscan \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.\n\nFor more details and further functionality, please refer to the usage documentation and the parameter documentation.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\noutput documentation.\n\n## Credits\n\nnf-core/funcscan was originally written by Jasmin Frangenberg, Anan Ibrahim, Louisa Perelo, Moritz E. Beber, James A. Fellows Yates.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n If applicable, make list of people who have also contributed \n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the contributing guidelines.\n\nFor further information or help, don't hesitate to get in touch on the Slack #funcscan channel (you can join with this invite).\n\n## Citations\n\n Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. \n If you use nf-core/funcscan for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX \n\n Add bibliography of tools and data used in your pipeline \n\nAn extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.\n\nYou can cite the nf-core publication as follows:\n\n> The nf-core framework for community-curated bioinformatics pipelines.\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.\n",
• local_component_structure - merge_taxonomy_combgc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - merge_taxonomy_hamronization.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - merge_taxonomy_ampcombi.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - combgc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - amp_database_download.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - annotation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - bgc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - amp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - taxa_class.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - arg.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

• actions_ci - actions_ci

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .gitignore
• files_exist - File found: .nf-core.yml
• files_exist - File found: .editorconfig
• files_exist - File found: .prettierignore
• files_exist - File found: .prettierrc.yml
• files_exist - File found: CHANGELOG.md
• files_exist - File found: CITATIONS.md
• files_exist - File found: CODE_OF_CONDUCT.md
• files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_exist - File found: nextflow_schema.json
• files_exist - File found: nextflow.config
• files_exist - File found: README.md
• files_exist - File found: .github/.dockstore.yml
• files_exist - File found: .github/CONTRIBUTING.md
• files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
• files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
• files_exist - File found: .github/workflows/branch.yml
• files_exist - File found: .github/workflows/ci.yml
• files_exist - File found: .github/workflows/linting_comment.yml
• files_exist - File found: .github/workflows/linting.yml
• files_exist - File found: assets/email_template.html
• files_exist - File found: assets/email_template.txt
• files_exist - File found: assets/sendmail_template.txt
• files_exist - File found: assets/nf-core-funcscan_logo_light.png
• files_exist - File found: conf/modules.config
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• files_exist - File found: docs/images/nf-core-funcscan_logo_light.png
• files_exist - File found: docs/images/nf-core-funcscan_logo_dark.png
• files_exist - File found: docs/output.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/usage.md
• files_exist - File found: main.nf
• files_exist - File found: assets/multiqc_config.yml
• files_exist - File found: conf/base.config
• files_exist - File found: .github/workflows/awstest.yml
• files_exist - File found: .github/workflows/awsfulltest.yml
• files_exist - File found: modules.json
• files_exist - File found: ro-crate-metadata.json
• files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
• files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
• files_exist - File not found check: .github/workflows/push_dockerhub.yml
• files_exist - File not found check: .markdownlint.yml
• files_exist - File not found check: .nf-core.yaml
• files_exist - File not found check: .yamllint.yml
• files_exist - File not found check: bin/markdown_to_html.r
• files_exist - File not found check: conf/aws.config
• files_exist - File not found check: docs/images/nf-core-funcscan_logo.png
• files_exist - File not found check: lib/Checks.groovy
• files_exist - File not found check: lib/Completion.groovy
• files_exist - File not found check: lib/NfcoreTemplate.groovy
• files_exist - File not found check: lib/Utils.groovy
• files_exist - File not found check: lib/Workflow.groovy
• files_exist - File not found check: lib/WorkflowMain.groovy
• files_exist - File not found check: lib/WorkflowFuncscan.groovy
• files_exist - File not found check: parameters.settings.json
• files_exist - File not found check: pipeline_template.yml
• files_exist - File not found check: Singularity
• files_exist - File not found check: lib/nfcore_external_java_deps.jar
• files_exist - File not found check: .travis.yml
• nextflow_config - Found nf-schema plugin
• nextflow_config - Config variable found: manifest.name
• nextflow_config - Config variable found: manifest.nextflowVersion
• nextflow_config - Config variable found: manifest.description
• nextflow_config - Config variable found: manifest.version
• nextflow_config - Config variable found: manifest.homePage
• nextflow_config - Config variable found: timeline.enabled
• nextflow_config - Config variable found: trace.enabled
• nextflow_config - Config variable found: report.enabled
• nextflow_config - Config variable found: dag.enabled
• nextflow_config - Config variable found: process.cpus
• nextflow_config - Config variable found: process.memory
• nextflow_config - Config variable found: process.time
• nextflow_config - Config variable found: params.outdir
• nextflow_config - Config variable found: params.input
• nextflow_config - Config variable found: validation.help.enabled
• nextflow_config - Config variable found: manifest.mainScript
• nextflow_config - Config variable found: timeline.file
• nextflow_config - Config variable found: trace.file
• nextflow_config - Config variable found: report.file
• nextflow_config - Config variable found: dag.file
• nextflow_config - Config variable found: validation.help.beforeText
• nextflow_config - Config variable found: validation.help.afterText
• nextflow_config - Config variable found: validation.help.command
• nextflow_config - Config variable found: validation.summary.beforeText
• nextflow_config - Config variable found: validation.summary.afterText
• nextflow_config - Config variable (correctly) not found: params.nf_required_version
• nextflow_config - Config variable (correctly) not found: params.container
• nextflow_config - Config variable (correctly) not found: params.singleEnd
• nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
• nextflow_config - Config variable (correctly) not found: params.name
• nextflow_config - Config variable (correctly) not found: params.enable_conda
• nextflow_config - Config variable (correctly) not found: params.max_cpus
• nextflow_config - Config variable (correctly) not found: params.max_memory
• nextflow_config - Config variable (correctly) not found: params.max_time
• nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
• nextflow_config - Config variable (correctly) not found: params.validationLenientMode
• nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
• nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
• nextflow_config - Config timeline.enabled had correct value: true
• nextflow_config - Config report.enabled had correct value: true
• nextflow_config - Config trace.enabled had correct value: true
• nextflow_config - Config dag.enabled had correct value: true
• nextflow_config - Config manifest.name began with nf-core/
• nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
• nextflow_config - Config dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config manifest.version ends in dev: 2.1.0dev
• nextflow_config - Config params.custom_config_version is set to master
• nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Lines for loading custom profiles found
• nextflow_config - nextflow.config contains configuration profile test
• nextflow_config - Config default value correct: params.taxa_classification_tool= mmseqs2
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_compressed= 0
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_db_id= Kalamari
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_searchtype= 2
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_lcaranks= kingdom,phylum,class,order,family,genus,species
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_taxlineage= 1
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_sensitivity= 5.0
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_orffilters= 2.0
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_lcamode= 3
• nextflow_config - Config default value correct: params.taxa_classification_mmseqs_taxonomy_votemode= 1
• nextflow_config - Config default value correct: params.annotation_tool= pyrodigal
• nextflow_config - Config default value correct: params.annotation_bakta_db_downloadtype= full
• nextflow_config - Config default value correct: params.annotation_bakta_mincontiglen= 1
• nextflow_config - Config default value correct: params.annotation_bakta_translationtable= 11
• nextflow_config - Config default value correct: params.annotation_bakta_gram= ?
• nextflow_config - Config default value correct: params.annotation_prokka_kingdom= Bacteria
• nextflow_config - Config default value correct: params.annotation_prokka_gcode= 11
• nextflow_config - Config default value correct: params.annotation_prokka_mincontiglen= 1
• nextflow_config - Config default value correct: params.annotation_prokka_evalue= 1e-06
• nextflow_config - Config default value correct: params.annotation_prokka_coverage= 80
• nextflow_config - Config default value correct: params.annotation_prokka_compliant= true
• nextflow_config - Config default value correct: params.annotation_prodigal_transtable= 11
• nextflow_config - Config default value correct: params.annotation_pyrodigal_transtable= 11
• nextflow_config - Config default value correct: params.annotation_pyrodigal_stopcodon= false
• nextflow_config - Config default value correct: params.amp_ampir_model= precursor
• nextflow_config - Config default value correct: params.amp_ampir_minlength= 10
• nextflow_config - Config default value correct: params.amp_ampcombi_db_id= DRAMP
• nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_cutoff= 0.6
• nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_aalength= 120
• nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_dbevalue= 5.0
• nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_hmmevalue= 0.06
• nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_windowstopcodon= 60
• nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_windowtransport= 11
• nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_ampir= .ampir.tsv
• nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_amplify= .amplify.tsv
• nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_macrel= .macrel.prediction
• nextflow_config - Config default value correct: params.amp_ampcombi_parsetables_hmmsearch= .hmmer_hmmsearch.txt
• nextflow_config - Config default value correct: params.amp_ampcombi_cluster_covmode= 0.0
• nextflow_config - Config default value correct: params.amp_ampcombi_cluster_sensitivity= 4.0
• nextflow_config - Config default value correct: params.amp_ampcombi_cluster_minmembers= 0
• nextflow_config - Config default value correct: params.amp_ampcombi_cluster_mode= 1.0
• nextflow_config - Config default value correct: params.amp_ampcombi_cluster_coverage= 0.8
• nextflow_config - Config default value correct: params.amp_ampcombi_cluster_seqid= 0.4
• nextflow_config - Config default value correct: params.arg_amrfinderplus_identmin= -1.0
• nextflow_config - Config default value correct: params.arg_amrfinderplus_coveragemin= 0.5
• nextflow_config - Config default value correct: params.arg_amrfinderplus_translationtable= 11
• nextflow_config - Config default value correct: params.arg_deeparg_db_version= 2
• nextflow_config - Config default value correct: params.arg_deeparg_model= LS
• nextflow_config - Config default value correct: params.arg_deeparg_minprob= 0.8
• nextflow_config - Config default value correct: params.arg_deeparg_alignmentevalue= 1e-10
• nextflow_config - Config default value correct: params.arg_deeparg_alignmentidentity= 50
• nextflow_config - Config default value correct: params.arg_deeparg_alignmentoverlap= 0.8
• nextflow_config - Config default value correct: params.arg_deeparg_numalignmentsperentry= 1000
• nextflow_config - Config default value correct: params.arg_fargene_hmmmodel= class_a,class_b_1_2,class_b_3,class_c,class_d_1,class_d_2,qnr,tet_efflux,tet_rpg,tet_enzyme
• nextflow_config - Config default value correct: params.arg_fargene_minorflength= 90
• nextflow_config - Config default value correct: params.arg_fargene_translationformat= pearson
• nextflow_config - Config default value correct: params.arg_rgi_alignmenttool= BLAST
• nextflow_config - Config default value correct: params.arg_rgi_data= NA
• nextflow_config - Config default value correct: params.arg_rgi_split_prodigal_jobs= true
• nextflow_config - Config default value correct: params.arg_abricate_db_id= ncbi
• nextflow_config - Config default value correct: params.arg_abricate_minid= 80
• nextflow_config - Config default value correct: params.arg_abricate_mincov= 80
• nextflow_config - Config default value correct: params.arg_hamronization_summarizeformat= tsv
• nextflow_config - Config default value correct: params.bgc_mincontiglength= 3000
• nextflow_config - Config default value correct: params.bgc_antismash_contigminlength= 3000
• nextflow_config - Config default value correct: params.bgc_antismash_hmmdetectionstrictness= relaxed
• nextflow_config - Config default value correct: params.bgc_antismash_taxon= bacteria
• nextflow_config - Config default value correct: params.bgc_deepbgc_score= 0.5
• nextflow_config - Config default value correct: params.bgc_deepbgc_mergemaxproteingap= 0
• nextflow_config - Config default value correct: params.bgc_deepbgc_mergemaxnuclgap= 0
• nextflow_config - Config default value correct: params.bgc_deepbgc_minnucl= 1
• nextflow_config - Config default value correct: params.bgc_deepbgc_minproteins= 1
• nextflow_config - Config default value correct: params.bgc_deepbgc_mindomains= 1
• nextflow_config - Config default value correct: params.bgc_deepbgc_minbiodomains= 0
• nextflow_config - Config default value correct: params.bgc_deepbgc_classifierscore= 0.5
• nextflow_config - Config default value correct: params.bgc_gecco_cds= 3
• nextflow_config - Config default value correct: params.bgc_gecco_pfilter= 1e-09
• nextflow_config - Config default value correct: params.bgc_gecco_threshold= 0.8
• nextflow_config - Config default value correct: params.bgc_gecco_edgedistance= 0
• nextflow_config - Config default value correct: params.custom_config_version= master
• nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Config default value correct: params.publish_dir_mode= copy
• nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
• nextflow_config - Config default value correct: params.validate_params= true
• nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - CODE_OF_CONDUCT.md matches the template
• files_unchanged - LICENSE matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/CONTRIBUTING.md matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
• files_unchanged - .github/workflows/branch.yml matches the template
• files_unchanged - .github/workflows/linting_comment.yml matches the template
• files_unchanged - .github/workflows/linting.yml matches the template
• files_unchanged - assets/email_template.html matches the template
• files_unchanged - assets/email_template.txt matches the template
• files_unchanged - assets/sendmail_template.txt matches the template
• files_unchanged - assets/nf-core-funcscan_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-funcscan_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-funcscan_logo_dark.png matches the template
• files_unchanged - docs/README.md matches the template
• files_unchanged - .gitignore matches the template
• files_unchanged - .prettierignore matches the template
• actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
• actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
• actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
• readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
• readme - README Zenodo placeholder was replaced with DOI.
• plugin_includes - No wrong validation plugin imports have been found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (0 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: template_version_comment.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• multiqc_config - assets/multiqc_config.yml found and not ignored.
• multiqc_config - assets/multiqc_config.yml contains report_section_order
• multiqc_config - assets/multiqc_config.yml contains export_plots
• multiqc_config - assets/multiqc_config.yml contains report_comment
• multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
• multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
• multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• base_config - GUNZIP found in conf/base.config and Nextflow scripts.
• base_config - UNTAR found in conf/base.config and Nextflow scripts.
• base_config - PROKKA found in conf/base.config and Nextflow scripts.
• base_config - PRODIGAL_GBK found in conf/base.config and Nextflow scripts.
• base_config - BAKTA_BAKTA found in conf/base.config and Nextflow scripts.
• base_config - ABRICATE_RUN found in conf/base.config and Nextflow scripts.
• base_config - AMRFINDERPLUS_RUN found in conf/base.config and Nextflow scripts.
• base_config - DEEPARG_DOWNLOADDATA found in conf/base.config and Nextflow scripts.
• base_config - DEEPARG_PREDICT found in conf/base.config and Nextflow scripts.
• base_config - FARGENE found in conf/base.config and Nextflow scripts.
• base_config - RGI_MAIN found in conf/base.config and Nextflow scripts.
• base_config - AMPIR found in conf/base.config and Nextflow scripts.
• base_config - AMPLIFY_PREDICT found in conf/base.config and Nextflow scripts.
• base_config - AMP_HMMER_HMMSEARCH found in conf/base.config and Nextflow scripts.
• base_config - MACREL_CONTIGS found in conf/base.config and Nextflow scripts.
• base_config - BGC_HMMER_HMMSEARCH found in conf/base.config and Nextflow scripts.
• base_config - ANTISMASH_ANTISMASHLITE found in conf/base.config and Nextflow scripts.
• base_config - ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES found in conf/base.config and Nextflow scripts.
• base_config - DEEPBGC_DOWNLOAD found in conf/base.config and Nextflow scripts.
• base_config - DEEPBGC_PIPELINE found in conf/base.config and Nextflow scripts.
• base_config - GECCO_RUN found in conf/base.config and Nextflow scripts.
• base_config - HAMRONIZATION_ABRICATE found in conf/base.config and Nextflow scripts.
• base_config - HAMRONIZATION_AMRFINDERPLUS found in conf/base.config and Nextflow scripts.
• base_config - HAMRONIZATION_DEEPARG found in conf/base.config and Nextflow scripts.
• base_config - HAMRONIZATION_RGI found in conf/base.config and Nextflow scripts.
• base_config - HAMRONIZATION_FARGENE found in conf/base.config and Nextflow scripts.
• base_config - HAMRONIZATION_SUMMARIZE found in conf/base.config and Nextflow scripts.
• base_config - ARGNORM_DEEPARG found in conf/base.config and Nextflow scripts.
• base_config - ARGNORM_ABRICATE found in conf/base.config and Nextflow scripts.
• base_config - ARGNORM_AMRFINDERPLUS found in conf/base.config and Nextflow scripts.
• base_config - AMPCOMBI2_PARSETABLES found in conf/base.config and Nextflow scripts.
• base_config - AMPCOMBI2_CLUSTER found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - GUNZIP found in conf/modules.config and Nextflow scripts.
• modules_config - MMSEQS_DATABASES found in conf/modules.config and Nextflow scripts.
• modules_config - MMSEQS_CREATEDB found in conf/modules.config and Nextflow scripts.
• modules_config - MMSEQS_TAXONOMY found in conf/modules.config and Nextflow scripts.
• modules_config - MMSEQS_CREATETSV found in conf/modules.config and Nextflow scripts.
• modules_config - SEQKIT_SEQ found in conf/modules.config and Nextflow scripts.
• modules_config - PROKKA found in conf/modules.config and Nextflow scripts.
• modules_config - BAKTA_BAKTADBDOWNLOAD found in conf/modules.config and Nextflow scripts.
• modules_config - BAKTA_BAKTA found in conf/modules.config and Nextflow scripts.
• modules_config - PRODIGAL found in conf/modules.config and Nextflow scripts.
• modules_config - PYRODIGAL found in conf/modules.config and Nextflow scripts.
• modules_config - ABRICATE_RUN found in conf/modules.config and Nextflow scripts.
• modules_config - AMRFINDERPLUS_UPDATE found in conf/modules.config and Nextflow scripts.
• modules_config - AMRFINDERPLUS_RUN found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPARG_DOWNLOADDATA found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPARG_PREDICT found in conf/modules.config and Nextflow scripts.
• modules_config - FARGENE found in conf/modules.config and Nextflow scripts.
• modules_config - UNTAR_CARD found in conf/modules.config and Nextflow scripts.
• modules_config - RGI_CARDANNOTATION found in conf/modules.config and Nextflow scripts.
• modules_config - RGI_MAIN found in conf/modules.config and Nextflow scripts.
• modules_config - AMPIR found in conf/modules.config and Nextflow scripts.
• modules_config - AMPLIFY_PREDICT found in conf/modules.config and Nextflow scripts.
• modules_config - AMP_HMMER_HMMSEARCH found in conf/modules.config and Nextflow scripts.
• modules_config - MACREL_CONTIGS found in conf/modules.config and Nextflow scripts.
• modules_config - BGC_HMMER_HMMSEARCH found in conf/modules.config and Nextflow scripts.
• modules_config - ANTISMASH_ANTISMASHLITE found in conf/modules.config and Nextflow scripts.
• modules_config - ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPBGC_DOWNLOAD found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPBGC_PIPELINE found in conf/modules.config and Nextflow scripts.
• modules_config - GECCO_RUN found in conf/modules.config and Nextflow scripts.
• modules_config - HAMRONIZATION_ABRICATE found in conf/modules.config and Nextflow scripts.
• modules_config - HAMRONIZATION_AMRFINDERPLUS found in conf/modules.config and Nextflow scripts.
• modules_config - HAMRONIZATION_DEEPARG found in conf/modules.config and Nextflow scripts.
• modules_config - HAMRONIZATION_RGI found in conf/modules.config and Nextflow scripts.
• modules_config - HAMRONIZATION_FARGENE found in conf/modules.config and Nextflow scripts.
• modules_config - HAMRONIZATION_SUMMARIZE found in conf/modules.config and Nextflow scripts.
• modules_config - MERGE_TAXONOMY_HAMRONIZATION found in conf/modules.config and Nextflow scripts.
• modules_config - ARG_TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
• modules_config - AMPCOMBI2_PARSETABLES found in conf/modules.config and Nextflow scripts.
• modules_config - AMPCOMBI2_COMPLETE found in conf/modules.config and Nextflow scripts.
• modules_config - AMPCOMBI2_CLUSTER found in conf/modules.config and Nextflow scripts.
• modules_config - MERGE_TAXONOMY_AMPCOMBI found in conf/modules.config and Nextflow scripts.
• modules_config - AMP_TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
• modules_config - COMBGC found in conf/modules.config and Nextflow scripts.
• modules_config - ARGNORM_ABRICATE found in conf/modules.config and Nextflow scripts.
• modules_config - ARGNORM_AMRFINDERPLUS found in conf/modules.config and Nextflow scripts.
• modules_config - ARGNORM_DEEPARG found in conf/modules.config and Nextflow scripts.
• modules_config - MERGE_TAXONOMY_COMBGC found in conf/modules.config and Nextflow scripts.
• modules_config - BGC_TABIX_BGZIP found in conf/modules.config and Nextflow scripts.
• modules_config - AMP_DATABASE_DOWNLOAD found in conf/modules.config and Nextflow scripts.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
• nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.2.0

Run details

• nf-core/tools version 3.2.0
• Run at 2025-02-04 16:17:31

[jfy133]

See comment about Param name otherwise lgtm

[jfy133]

The pipeline flag should also be nostopcodon so it's clearer to the user

[jasmezz]

Okay, is more intuitive yes. On the other hand I wanted to stick to the "codex" to have params default to false in the nextflow.config (the renamed annotation_pyrodigal_nostopcodon would have to be true by default).

[jasmezz]

Oh I just saw that I flipped the logic by mistake 🙈 I'll update the above line to
params.annotation_pyrodigal_stopcodon ? '' : '--no-stop-codon',