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Restore the Workflow block in the software versions YAML - #469

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NicoDeVeaux:fix-versions-yaml-workflow-block
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Restore the Workflow block in the software versions YAML#469
NicoDeVeaux wants to merge 1 commit into
nf-core:devfrom
NicoDeVeaux:fix-versions-yaml-workflow-block

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@NicoDeVeaux

@NicoDeVeaux NicoDeVeaux commented Oct 7, 2026 •
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Collecting versions from the topic channel (#448) dropped the softwareVersionsToYAML() call, which also appended workflowVersionToYAML(): the pipeline and Nextflow versions. Mix it back in before collectFile, and restore the Workflow entry that #448's snapshot update removed from the nf-test snapshots.

The fix restores exactly the .mix(channel.of(workflowVersionToYAML())) that the template helper does.

Where it appears: in two places.

  1. The file: /pipeline_info/nf_core_atacseq_software_mqc_versions.yml. With the fix, it ends with this block, from workflowVersionToYAML() in subworkflows/nf-core/utils_nfcore_pipeline/main.nf:89:
    Workflow:
    nf-core/atacseq: v2.2.0dev
    Nextflow: 26.04.6
  2. The MultiQC report: the _mqc suffix makes MultiQC read the file into its "Software Versions" table. Without the block, that table lists every tool but not which pipeline version or Nextflow version produced the report.

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/atacseq 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>).
  • 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).

@NicoDeVeaux @claude
Restore the Workflow block in the software versions YAML
8af5326 
Collecting versions from the topic channel (nf-core#448) dropped the
softwareVersionsToYAML() call, which also appended workflowVersionToYAML():
the pipeline and Nextflow versions. Mix it back in before collectFile, and
restore the Workflow entry that nf-core#448's snapshot update removed from the
nf-test snapshots.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

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github-actions Bot commented Oct 7, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8af5326

+| ✅ 274 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  37 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 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 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 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • local_component_structure - get_autosomes.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bamtools_filter.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - multiqc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - star_genomegenerate.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - samplesheet_check.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - tss_extract.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bam_remove_orphans.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - plot_homer_annotatepeaks.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - igv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - star_align.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - macs3_consensus.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - frip_score.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - genome_blacklist_regions.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - multiqc_custom_peaks.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - gtf2bed.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bedtools_genomecov.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - plot_macs3_qc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - deseq2_qc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bigwig_plot_deeptools.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bam_filter_bamtools.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bam_bedgraph_bigwig_bedtools_ucsc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bam_peaks_call_qc_annotate_macs3_homer.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bam_shift_reads.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - align_star.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • merge_markers - Ignoring file /home/runner/work/atacseq/atacseq/modules/nf-core/bowtie2/align/tests/main.nf.test.snap

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.3
  • Run at 2026-10-07 13:18:05

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@NicoDeVeaux