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Follow up to 487#493

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Kevin-Brockers merged 19 commits intonf-core:devfrom
JoseEspinosa:fixes
Mar 25, 2026
Merged

Follow up to 487#493
Kevin-Brockers merged 19 commits intonf-core:devfrom
JoseEspinosa:fixes

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@JoseEspinosa JoseEspinosa commented Mar 19, 2026 •
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Follow-up to PR #487 (topic channel adaptation). This PR addresses issues found during review and cleans up the codebase after the module updates.

  • Fix ch_versions collection: ch_versions was initialized as channel.empty() and never populated, meaning all modules still using the traditional versions.yml pattern had their versions silently dropped from the final report. Added version collection from PREPARE_GENOME, INPUT_CHECK, BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER, BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2, and IGV into ch_versions so they are included in softwareVersionsToYAML().
  • Remove unnecessary saveAs filters from all modules that were converted to topic channels (no longer produce versions.yml).
  • Merged multiple separate process {} blocks into a single closure with section comments in nextflow.config.
  • Publish files produced by SAMTOOLS_FAIDX in genome folder as CUSTOM_GETCHROMSIZES did.
  • Clean changelog.

PR checklist

  • This comment contains a description of changes (with reason).
  • 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>).
  • CHANGELOG.md is updated.

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github-actions bot commented Mar 19, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e548d1f

+| ✅ 267 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   7 tests had warnings |!
Details

❗ Test warnings:

  • 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 base.config: Check the defaults for all processes
  • 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!

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-03-23 21:35:24

@JoseEspinosa JoseEspinosa changed the title Follow up to 483 Follow up to 487 Mar 23, 2026
@JoseEspinosa JoseEspinosa marked this pull request as ready for review March 23, 2026 21:45
@Kevin-Brockers Kevin-Brockers self-requested a review March 24, 2026 15:45
Kevin-Brockers
Kevin-Brockers approved these changes Mar 25, 2026
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Looks good to me

@Kevin-Brockers Kevin-Brockers merged commit 643351e into nf-core:dev Mar 25, 2026
20 checks passed
Kevin-Brockers added a commit to Kevin-Brockers/chipseq that referenced this pull request Mar 26, 2026
@Kevin-Brockers
merged nf-core#493 PR in local dev
7f4d342
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