Template update to 3.4.1

[famosab]

PR checklist

Closes #29

• 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/variantprioritization branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines 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 da6ae01

+| ✅ 235 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  81 tests had warnings |!

❗ Test warnings:

• readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
• pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
• pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
• pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
• pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
• pipeline_todos - TODO string in base.config: Check the defaults for all processes
• pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
• pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
• pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
• pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
• pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
• pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
• pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
• pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
• pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
• pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
• pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
• pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
• schema_description - Ungrouped param in schema: save_intermediates
• schema_description - Ungrouped param in schema: database
• schema_description - Ungrouped param in schema: vep_cache
• schema_description - Ungrouped param in schema: panel_id
• schema_description - Ungrouped param in schema: diagnostic_grade_only
• schema_description - Ungrouped param in schema: ignore_noncoding
• schema_description - Ungrouped param in schema: pop_gnomad
• schema_description - Ungrouped param in schema: maf_upper_threshold
• schema_description - Ungrouped param in schema: classify_all
• schema_description - Ungrouped param in schema: clinvar_ignore_noncancer
• schema_description - Ungrouped param in schema: vcf2maf
• schema_description - Ungrouped param in schema: assay
• schema_description - Ungrouped param in schema: cpsr_report
• schema_description - Ungrouped param in schema: tumor_site
• schema_description - Ungrouped param in schema: tumor_purity
• schema_description - Ungrouped param in schema: tumor_ploidy
• schema_description - Ungrouped param in schema: cna_analysis
• schema_description - Ungrouped param in schema: cna_overlap_pct
• schema_description - Ungrouped param in schema: effective_target_size_mb
• schema_description - Ungrouped param in schema: estimate_tmb
• schema_description - Ungrouped param in schema: estimate_msi
• schema_description - Ungrouped param in schema: tmb_display
• schema_description - Ungrouped param in schema: estimate_signatures
• schema_description - Ungrouped param in schema: min_mutations_signatures
• schema_description - Ungrouped param in schema: all_reference_signatures
• schema_description - Ungrouped param in schema: include_artefact_signatures
• schema_description - Ungrouped param in schema: prevalence_reference_signatures
• schema_description - Ungrouped param in schema: include_trials
• schema_description - Ungrouped param in schema: tumor_dp_min
• schema_description - Ungrouped param in schema: tumor_af_min
• schema_description - Ungrouped param in schema: control_dp_min
• schema_description - Ungrouped param in schema: control_af_max
• schema_description - Ungrouped param in schema: tumor_only
• schema_description - Ungrouped param in schema: pon_vcf
• schema_description - Ungrouped param in schema: exclude_pon
• schema_description - Ungrouped param in schema: exclude_likely_hom_germline
• schema_description - Ungrouped param in schema: exclude_likely_het_germline
• schema_description - Ungrouped param in schema: exclude_dbsnp_nonsomatic
• schema_description - Ungrouped param in schema: exclude_nonexonic
• schema_description - Ungrouped param in schema: maf_gnomad_nfe
• schema_description - Ungrouped param in schema: maf_gnomad_fin
• schema_description - Ungrouped param in schema: maf_gnomad_asj
• schema_description - Ungrouped param in schema: maf_gnomad_oth
• schema_description - Ungrouped param in schema: maf_gnomad_amr
• schema_description - Ungrouped param in schema: maf_gnomad_afr
• schema_description - Ungrouped param in schema: maf_gnomad_eas
• schema_description - Ungrouped param in schema: maf_gnomad_sas
• schema_description - Ungrouped param in schema: maf_gnomad_global
• schema_description - Ungrouped param in schema: filter_haplotypecaller
• schema_description - Ungrouped param in schema: filter_deepvariant
• schema_description - Ungrouped param in schema: filter_strelka_variants
• schema_description - Ungrouped param in schema: filter_freebayes_germline
• schema_description - Ungrouped param in schema: filter_mutect2
• schema_description - Ungrouped param in schema: filter_freebayes_somatic
• schema_description - Ungrouped param in schema: filter_strelka_indels
• schema_description - Ungrouped param in schema: filter_strelka_snvs
• schema_description - Ungrouped param in schema: vep_n_forks
• schema_description - Ungrouped param in schema: vep_buffer_size
• schema_description - Ungrouped param in schema: vep_gencode_all
• schema_description - Ungrouped param in schema: vep_pick_order
• schema_description - Ungrouped param in schema: vep_no_intergenic
• local_component_structure - format_files.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - vcf_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

• files_exist - File is ignored: .github/workflows/ci.yml
• files_unchanged - File ignored due to lint config: assets/nf-core-variantprioritization_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-variantprioritization_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-variantprioritization_logo_dark.png
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .gitignore
• files_exist - File found: .nf-core.yml
• 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/nf-test.yml
• files_exist - File found: .github/actions/get-shards/action.yml
• files_exist - File found: .github/actions/nf-test/action.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-variantprioritization_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-variantprioritization_logo_light.png
• files_exist - File found: docs/images/nf-core-variantprioritization_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: nf-test.config
• files_exist - File found: tests/default.nf.test
• 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: conf/igenomes.config
• files_exist - File found: conf/igenomes_ignored.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-variantprioritization_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/WorkflowVariantprioritization.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: 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 (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 variable (correctly) not found: validation.failUnrecognisedParams
• nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
• 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: 1.0.0dev
• 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.panel_id= 0
• nextflow_config - Config default value correct: params.pop_gnomad= nfe
• nextflow_config - Config default value correct: params.maf_upper_threshold= 0.9
• nextflow_config - Config default value correct: params.tumor_site= 0
• nextflow_config - Config default value correct: params.cna_overlap_pct= 50
• nextflow_config - Config default value correct: params.effective_target_size_mb= 34
• nextflow_config - Config default value correct: params.tmb_display= coding_and_silent
• nextflow_config - Config default value correct: params.min_mutations_signatures= 200
• nextflow_config - Config default value correct: params.prevalence_reference_signatures= 5
• nextflow_config - Config default value correct: params.include_trials= true
• nextflow_config - Config default value correct: params.tumor_dp_min= 0
• nextflow_config - Config default value correct: params.tumor_af_min= 0
• nextflow_config - Config default value correct: params.control_dp_min= 0
• nextflow_config - Config default value correct: params.control_af_max= 1
• nextflow_config - Config default value correct: params.maf_gnomad_nfe= 0.002
• nextflow_config - Config default value correct: params.maf_gnomad_fin= 0.002
• nextflow_config - Config default value correct: params.maf_gnomad_asj= 0.002
• nextflow_config - Config default value correct: params.maf_gnomad_oth= 0.002
• nextflow_config - Config default value correct: params.maf_gnomad_amr= 0.002
• nextflow_config - Config default value correct: params.maf_gnomad_afr= 0.002
• nextflow_config - Config default value correct: params.maf_gnomad_eas= 0.002
• nextflow_config - Config default value correct: params.maf_gnomad_sas= 0.002
• nextflow_config - Config default value correct: params.maf_gnomad_global= 0.002
• nextflow_config - Config default value correct: params.filter_haplotypecaller= -i'FORMAT/DP>10\
• nextflow_config - Config default value correct: params.filter_deepvariant= -i'FORMAT/DP>10\
• nextflow_config - Config default value correct: params.filter_strelka_variants= -i'FORMAT/DP>10\
• nextflow_config - Config default value correct: params.filter_freebayes_germline= -i'FORMAT/DP>10\
• nextflow_config - Config default value correct: params.filter_mutect2= -i'FORMAT/DP>10\
• nextflow_config - Config default value correct: params.filter_freebayes_somatic= -i'FORMAT/DP>10\
• nextflow_config - Config default value correct: params.filter_strelka_indels= -i'FORMAT/DP>10\
• nextflow_config - Config default value correct: params.filter_strelka_snvs= -i'FORMAT/DP>10\
• nextflow_config - Config default value correct: params.vep_n_forks= 4
• nextflow_config - Config default value correct: params.vep_buffer_size= 500
• nextflow_config - Config default value correct: params.vep_gencode_all= true
• nextflow_config - Config default value correct: params.vep_pick_order= mane_select,mane_plus_clinical,canonical,biotype,ccds,rank,tsl,appris,length
• nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
• 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/
• nf_test_content - 'tests/default.nf.test' contains outdir parameter
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
• nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
• nf_test_content - 'nf-test.config' sets a testsDir
• nf_test_content - 'nf-test.config' sets a workDir
• nf_test_content - 'nf-test.config' sets a configFile
• 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 - docs/README.md matches the template
• actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
• actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
• 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: 25.04.0, Config: 25.04.0
• readme - README nf-core template version badge found.
• pipeline_if_empty_null - No ifEmpty(null) strings found
• 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: linting.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: clean-up.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'
• local_component_structure - local modules directory structure is correct 'modules/local/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• modules_config - conf/modules.config found and not ignored.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_NORM found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_FILTER found in conf/modules.config and Nextflow scripts.
• modules_config - REFORMAT_VCF found in conf/modules.config and Nextflow scripts.
• modules_config - REFORMAT_CNA found in conf/modules.config and Nextflow scripts.
• modules_config - INTERSECT_SOMATIC_VARIANTS found in conf/modules.config and Nextflow scripts.
• modules_config - PCGR_VCF found in conf/modules.config and Nextflow scripts.
• modules_config - PCGR 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: 3.4.1
• rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

• nf-core/tools version 3.4.1
• Run at 2025-10-28 14:17:40

[maxulysse]

minor comments

[famosab]

So we are getting md5sum mismatches for now - will merge this anyway (because someone else is working on a proper test setup with VEP cache an so on see #26)