fix: Update all modules and collect software versions with topic channels

[beatrizsavinhas]

Closes #31

Changed

• Refactored input for multiqc to conform to updated module requirements.

Fixed

• Updated all nf-core modules with nf-core modules update to implement latest nf-core changes that use the versions topic channel to collect the software versions:

   'nf-core/bcftools/annotate'                                                                                                                                            
   'nf-core/bcftools/filter' 
   'nf-core/bcftools/index'
   'nf-core/bcftools/view' 
   'nf-core/ensemblvep/vep' 
   'nf-core/multiqc'
   'nf-core/svdb/query'
   'nf-core/tabix/tabix'
   'nf-core/untar'
   'nf-core/vcfanno'
  

Removed

• Removed deprecated ch_versions from subworkflows/local/prepare_references.nf.

[github-actions]

PR checklist

• Fill in description of the PR and link to any relevant issues.
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool, follow the pipeline conventions in the contribution docs.
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.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 8eac197

+| ✅ 180 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗  28 tests had warnings |!

Details

❗ 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 README.md: TODO nf-core:
• pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
• pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline 2. Present QC for raw reads (MultiQC)
• pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
• 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 README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
• pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
• 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 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 nextflow.config: Specify any additional parameters here
• 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 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.config: Specify the paths to your test data on nf-core/test-datasets
• pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
• 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 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!
• schema_description - Ungrouped param in schema: snv_vcf
• schema_description - Ungrouped param in schema: sv_vcf
• schema_description - Ungrouped param in schema: custom_extra_files
• local_component_structure - prepare_references.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: conf/igenomes_ignored.config
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
• files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
• files_unchanged - File ignored due to lint config: docs/README.md
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
• actions_awstest - actions_awstest
• actions_awsfulltest - actions_awsfulltest
• multiqc_config - multiqc_config

✅ 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-oncorefiner_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-oncorefiner_logo_light.png
• files_exist - File found: docs/images/nf-core-oncorefiner_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: 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-oncorefiner_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/WorkflowOncorefiner.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 Clinical-Genomics/
• nextflow_config - Config variable manifest.homePage began with https://github.com/Clinical-Genomics/
• 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.genome= GRCh38
• nextflow_config - Config default value correct: params.vep_cache_version= 112
• 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/Clinical-Genomics/test-datasets/refs/heads/oncorefiner/
• 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 - LICENSE matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/CONTRIBUTING.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 - assets/email_template.html matches the template
• files_unchanged - assets/email_template.txt 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
• readme - README Nextflow minimum version badge matched config. Badge: 25.10.0, Config: 25.10.0
• 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: branch.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: add_pr_checklist_comment.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: conventional_pr_title.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: update_changelog.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• 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 - ENSEMBLVEP_SNV found in conf/modules.config and Nextflow scripts.
• modules_config - VCFANNO found in conf/modules.config and Nextflow scripts.
• modules_config - RESEARCH_FILTERING found in conf/modules.config and Nextflow scripts.
• modules_config - CLINICAL_FILTERING found in conf/modules.config and Nextflow scripts.
• modules_config - SVDB_QUERY_DB found in conf/modules.config and Nextflow scripts.
• modules_config - ENSEMBLVEP_SV found in conf/modules.config and Nextflow scripts.
• modules_config - RESEARCH_FILTERING_SV found in conf/modules.config and Nextflow scripts.
• modules_config - CLINICAL_FILTERING_SV 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: 3.5.2
• rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

• nf-core/tools version 3.5.2
• Run at 2026-03-10 11:58:43

[beatrizsavinhas]

Test

Command: nextflow run . -profile test,docker --outdir results
Result:

Software versions are now collected!

[kristinebilgrav]

Great job! Lots of nf-core module updates. Saw something with FastQC in the multiQC files that I was wondering about. Otherwise looks good! 🌟