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General modules update, include updating subworkflows for stats fixes #1560

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pinin4fjords merged 22 commits into from
Jun 4, 2025
Merged

General modules update, include updating subworkflows for stats fixes #1560

pinin4fjords merged 22 commits into from
Jun 4, 2025

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@pinin4fjords pinin4fjords commented Jun 4, 2025 •
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Pull in fixes from nf-core/modules#8577, nf-core/modules#8481, and other modules updates.

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/rnaseq 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).

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github-actions bot commented Jun 4, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9047700

+| ✅ 278 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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_if_empty_null - ifEmpty(null) found in main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.1
  • Run at 2025-06-04 19:09:05

@pinin4fjords pinin4fjords changed the title Fix stats parsing in FASTQ_FASTQC_UMITOOLS_TRIMGALORE Update subworkflows for stats fixes Jun 4, 2025
@pinin4fjords pinin4fjords linked an issue Jun 4, 2025 that may be closed by this pull request
getTrimGaloreReadsAfterFiltering function fails to extract filtered read count from TrimGalore log #1557
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@pinin4fjords pinin4fjords changed the title Update subworkflows for stats fixes General modules update, include updating subworkflows for stats fixes Jun 4, 2025
@pinin4fjords pinin4fjords mentioned this pull request Jun 4, 2025
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@pinin4fjords pinin4fjords mentioned this pull request Jun 4, 2025
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@pinin4fjords pinin4fjords merged commit 1323533 into dev Jun 4, 2025
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@pinin4fjords pinin4fjords deleted the add_trimgalore_stats_fix branch June 4, 2025 21:34
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getTrimGaloreReadsAfterFiltering function fails to extract filtered read count from TrimGalore log

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