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Fixed version reporting by ensure all modules are represented in final version.yml for MultiQC#852

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jfy133 merged 16 commits intodevfrom
fix-version-linting
Aug 25, 2025
Merged

Fixed version reporting by ensure all modules are represented in final version.yml for MultiQC#852
jfy133 merged 16 commits intodevfrom
fix-version-linting

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@jfy133 jfy133 commented Aug 22, 2025 •
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Closes #761

  • Add missings .mix(XXX.out.versions) where necessary
  • Add missing HEREDOCs in lcoa lmodules missing module versions.yml generation
  • Fixes missing first() on modules
  • Moves all version missing next to each module/subworkflow for consistency and better checking during reviewign
  • Nextflow-autoformatting

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/mag 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 Aug 22, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2fa3ac8

+| ✅ 363 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   6 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • 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 nextflow.config: Specify any additional parameters here
  • 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

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-08-25 18:48:20

prototaxites
prototaxites reviewed Aug 22, 2025
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Looks good! A few places where using .first() will likely produce a warning and should be removed? The rest are optional, though I would not be very concerned about the overhead of running .unique() personally.

Otherwise a couple of minor optional style things.

@jfy133 jfy133 requested a review from prototaxites August 22, 2025 12:30
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jfy133 commented Aug 22, 2025

OK all .first() removed, but I had to revert the ternary to if/else change because the nextflow autoformatter would remove the mode: bit breaking the operator... I don't know why... it's ugly but it's there

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prototaxites commented Aug 22, 2025

did you do it via sed? You've stripped .versions.first() rather than just .first()?

prototaxites
prototaxites reviewed Aug 22, 2025
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jfy133 commented Aug 22, 2025

So I think it's all working now @prototaxites !

I need to update the snapshots of each rest profile hwihc is going to take a looooooooooooooong time...

So maybe you can do one more pass before I start updating those?

prototaxites
prototaxites approved these changes Aug 22, 2025
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A few minor persnickety Harshill alignments if you can be bothered to fix them.

Otherwise looks good, happy to merge once you've done the snapshots!

@jfy133 jfy133 merged commit d349d5f into dev Aug 25, 2025
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@dialvarezs dialvarezs deleted the fix-version-linting branch November 21, 2025 11:36
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@prototaxites prototaxites prototaxites approved these changes

@d4straub d4straub Awaiting requested review from d4straub d4straub is a code owner

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

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

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@jfy133 @prototaxites @mahesh-panchal