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Update Modules #263

Merged
merged 11 commits into from
Oct 3, 2024
Merged

Update Modules #263

merged 11 commits into from
Oct 3, 2024

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apeltzer
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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 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 nh13, sam-white04 and a team as code owners September 17, 2024 14:32
@apeltzer apeltzer requested review from kobelavaerts and removed request for a team September 17, 2024 14:32
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github-actions bot commented Sep 17, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b40ecc6

+| ✅ 190 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.5.1
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • 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!
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-10-03 12:21:33

@apeltzer apeltzer requested review from atrigila and nschcolnicov and removed request for nh13, sam-white04 and kobelavaerts September 17, 2024 14:35
@nschcolnicov
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nschcolnicov commented Sep 24, 2024 •
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Seems like after the new MultiQC version, it no longer raises an error but the MultiQC report is still not displaying the Kraken section. The old issue explaining this is MultiQC/MultiQC#2801 and was closed after releasing version 1.25.

I created a new issue to follow up on the missing kraken report: MultiQC/MultiQC#2876

MultiQC report not displaying kraken:
image

@nschcolnicov
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I had to update some of the snaps, because the md5sums of some of the multiqc plots changed, due to them now displaying the numerical values with one decimal place:
image

nschcolnicov
nschcolnicov approved these changes Oct 3, 2024
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LGTM

@nschcolnicov nschcolnicov merged commit 3b2ef64 into dev Oct 3, 2024
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@nschcolnicov nschcolnicov mentioned this pull request Oct 7, 2024
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@grst grst mentioned this pull request Oct 7, 2024
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@atrigila atrigila atrigila approved these changes

@nschcolnicov nschcolnicov nschcolnicov approved these changes

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

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@apeltzer @nschcolnicov @atrigila