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Fix QUAST MultiQC config #752

Merged
merged 4 commits into from
Jan 22, 2025
Merged

Fix QUAST MultiQC config #752

merged 4 commits into from
Jan 22, 2025

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jfy133
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@jfy133 jfy133 commented Jan 22, 2025 •
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Close #741

Basically the fun_re was not picking up the files - I do not understand why though. Maybe it was because it was an invalid regex.

  • Includes another small fix to the MultiQC config because of a warning I noticed (adapterremoval mispelt)
  • And a language-server formatting of modules.config and mag.nf but there is no content changing there

Final thing:

  • ✅ I will do two tests of a 'normal' run and a skipping run to double check

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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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.1.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Jan 22, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b8b604b

+| ✅ 327 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ 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 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 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 passed:

Run details

  • nf-core/tools version 3.1.1
  • Run at 2025-01-22 10:44:18

@jfy133 jfy133 linked an issue Jan 22, 2025 that may be closed by this pull request
MultiQC is not consolidating QUAST reports for assemblies #741
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jfy133 commented Jan 22, 2025

Seems to work now:

Normal run
multiqc_report.zip

Skipping lots of things:
multiqc_report.zip

dialvarezs
dialvarezs approved these changes Jan 22, 2025
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LGTM!

@jfy133 jfy133 merged commit 1278ef3 into dev Jan 22, 2025
14 of 16 checks passed
@jfy133 jfy133 deleted the quast-results branch January 22, 2025 13:58
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@dialvarezs dialvarezs dialvarezs approved these changes

@d4straub d4straub Awaiting requested review from d4straub

@muabnezor muabnezor Awaiting requested review from muabnezor

@sateeshperi sateeshperi Awaiting requested review from sateeshperi

@amizeranschi amizeranschi Awaiting requested review from amizeranschi

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MultiQC is not consolidating QUAST reports for assemblies
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@jfy133 @nf-core-bot @dialvarezs