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Assorted fixes to MultiQC usage #1352

Merged
merged 16 commits into from
Aug 20, 2024
Merged

Assorted fixes to MultiQC usage #1352

merged 16 commits into from
Aug 20, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Aug 7, 2024 •
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This PR does a number of things related to issues identified in the MultiQC reporting:

  1. Static ordering for report components, set in the MultiQC config. I hate having to relocate something that have moved between runs, and I think it's easier to maintain if we have a static order we change at will (@drpatelh may have different views). The ordering I've set is in rough pipeline order, but we could rearrange.
  2. Reinstated trim failure reporting lost in previous PRs (whoops)
  3. Fixed methods reporting, also lost in structural changes since the last release
  4. Remove multiqcTsvFromList, now available via nf-core preprocessing subworkflow
  5. Group the related sample clustering plots
  6. Use replacement patterns to remove unnecessary suffixes trimmed, raw that were causing difficulties in the general stats.
  7. Bump MultiQC to incorporate a fix for software version reporting

There is a persistent issue with versions not being displayed, caused by MultiQC/MultiQC#2750, so we'll wait for resolution there before a merge. Now resolved

Differences between this and the current release can be seen in the attached reports.

multiqc_report_3_14.html.zip
multiqc_report_branch.html.zip

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 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).

@pinin4fjords pinin4fjords marked this pull request as draft August 7, 2024 15:51
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github-actions bot commented Aug 7, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 10a73f5

+| ✅ 173 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-20 09:33:54

@pinin4fjords pinin4fjords changed the title Try multiqc fixes Assorted fixes to MultiQC usage Aug 9, 2024
@pinin4fjords pinin4fjords marked this pull request as ready for review August 9, 2024 14:59
adamrtalbot
adamrtalbot approved these changes Aug 20, 2024
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Overall good!

The RNASEQ workflow is very overloaded, I am tempted to break things into subworkflows! 🤔

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The RNASEQ workflow is very overloaded, I am tempted to break things into subworkflows! 🤔

Agreed- I've already done that with the contentious preprocessing subworkflow ;-). But not now....

@pinin4fjords pinin4fjords added this to the 3.15.0 milestone Aug 20, 2024
maxulysse
maxulysse approved these changes Aug 20, 2024
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a pure thing of beauty

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Thanks @maxulysse @adamrtalbot !

@pinin4fjords pinin4fjords merged commit cb53ef3 into dev Aug 20, 2024
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@pinin4fjords pinin4fjords deleted the harmonize_new_for_multiqc branch August 20, 2024 09:53
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@adamrtalbot adamrtalbot adamrtalbot approved these changes

@maxulysse maxulysse maxulysse approved these changes

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen

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