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Add multiqc for metaphlan #600

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Merged
merged 6 commits into from
Apr 24, 2025
Merged

Add multiqc for metaphlan #600

merged 6 commits into from
Apr 24, 2025

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sofstam
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@sofstam sofstam commented Apr 17, 2025

Closes #597

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/taxprofiler 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).

@sofstam sofstam requested a review from a team April 17, 2025 08:26
jfy133
jfy133 reviewed Apr 17, 2025
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You need to specify metaphlan in the MuktiQC config file too, and possibly document in output.md if we do that. Otherwise also please check the verisio of multiqc we have supports it...

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sofstam commented Apr 17, 2025 •
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We have 1.27 version.

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jfy133 commented Apr 17, 2025

Should be good then! Latest is 1.28 but MetaPhlAn was added before then 👍

So just the confugration in the MQC config file then and possibly docs :)

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sofstam commented Apr 17, 2025

From test profile:

Screenshot 2025-04-17 at 14 24 11

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sofstam commented Apr 24, 2025

Docs and configuration updated.

@sofstam sofstam requested a review from jfy133 April 24, 2025 06:50
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Testing manually myself and it looks good to me, and is following our conventions in MultiQC report (e.g. no columns in general stats from profilers)

Only thing missing is the CHANGELOG entry (thanking @harper357 as usual)

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jfy133 commented Apr 24, 2025 •
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You can ignore all the latest-everything failed tests there is an issue in the nxf version - I'm going to remove them from required

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sofstam commented Apr 24, 2025

@nf-core-bot fix linting

@sofstam sofstam merged commit 6dd7b43 into nf-core:dev Apr 24, 2025
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