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Bump modules and subworkflows across entire pipeline#376

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apeltzer wants to merge 5 commits intodevfrom
update-modules
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Bump modules and subworkflows across entire pipeline#376
apeltzer wants to merge 5 commits intodevfrom
update-modules

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@apeltzer apeltzer commented Feb 26, 2026

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/demultiplex 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).

@apeltzer apeltzer requested review from a team, blajoie, nh13 and sam-white04 as code owners February 26, 2026 10:45
@apeltzer apeltzer requested review from Aratz and removed request for a team February 26, 2026 10:45
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apeltzer commented Feb 26, 2026

This should fix #374 and #338 @SPPearce

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github-actions bot commented Feb 26, 2026 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1f3bfed

+| ✅ 208 tests passed       |+
#| ❔   1 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • 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: Customise requirements for specific 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:

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-02-27 11:37:43

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apeltzer commented Feb 26, 2026

Yeah bunch of things to be done:

  • Versions topics

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SPPearce commented Feb 27, 2026

Interesting, as I was trying to do the same thing yesterday morning, but bcl_demultiplex was failing for me when it tries to classify each file as empty or not.

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SPPearce commented Feb 27, 2026

@matthdsm , I can't get your bcl_demultiplex to work inside demultiplex 😞

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matthdsm commented Feb 27, 2026

Are you using the latest version? I made some fixes earlier this week

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matthdsm reviewed Feb 27, 2026
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subworkflows/nf-core/bcl_demultiplex/main.nf Outdated
ch_interop = ch_interop.mix(BCLCONVERT.out.interop)
ch_reports = ch_reports.mix(BCLCONVERT.out.reports)
ch_logs = ch_logs.mix(BCLCONVERT.out.logs)
<<<<<<< Updated upstream
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Merge conflict, might be the cause of the issues 😄

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SPPearce commented Feb 27, 2026

Are you using the latest version? I made some fixes earlier this week

Yes, I am using your most recent version. Fixed the merge conflict, but can't seem to get it to work at the moment.

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matthdsm commented Feb 27, 2026

Looks like an issue nothing to do with bcl_demultiplex

    >   Item with id HBRR1_S1_L001 is missing the 'samplename' key. -- Check script '/home/runner/_work/demultiplex/demultiplex/modules/local/fastq_to_samplesheet/main.nf' at line: 28

@grst grst mentioned this pull request Apr 2, 2026
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@delfiterradas delfiterradas self-assigned this Apr 6, 2026
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@nh13 nh13 Awaiting requested review from nh13 nh13 is a code owner

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@blajoie blajoie Awaiting requested review from blajoie blajoie is a code owner

@Aratz Aratz Awaiting requested review from Aratz Aratz is a code owner automatically assigned from nf-core/demultiplex

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@apeltzer @SPPearce @matthdsm @grst @delfiterradas @nhcampbell