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Fixed multiqc report #76

Merged
merged 4 commits into from
Sep 15, 2024
Merged

Fixed multiqc report #76

merged 4 commits into from
Sep 15, 2024

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kbestak
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@kbestak kbestak commented Sep 9, 2024

Addresses #72
Added parameters necessary for create_training_subset to run with test.config for easier use.
Updated MultiQC version to 1.24.1
For easier testing in Gitpod, moved the Seqera Container for MultiQC to test.config instead of modules.config (as the Biocontainer cannot be pulled in Gitpod).
put .nf-test.log to .gitignore

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/molkart 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).

@kbestak kbestak requested a review from FloWuenne September 9, 2024 15:03
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github-actions bot commented Sep 9, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 07d44b1

+| ✅ 211 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • 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 passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-09 21:57:29

FloWuenne
FloWuenne requested changes Sep 9, 2024
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I went over the suggested changes and tested in Gitpod. Please address the few issues I have raised and afterward should be good to go. Main things:

  • Remove changelog, only use for releases
  • Don't do the test.config specification for the MultiQC container
  • Update multiQC docker container in modules.config instead!

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@kbestak
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kbestak commented Sep 9, 2024

Changelog removed - we update only for releases

Excluded Multiqc container as with 1.24.1 MultiQC version, the issue is fixed and I didn't catch that it was.

FloWuenne
FloWuenne approved these changes Sep 15, 2024
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LGTM now!

@kbestak kbestak merged commit b5aee86 into nf-core:dev Sep 15, 2024
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@kbestak kbestak deleted the multiqc_report_fix branch September 15, 2024 08:00
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@FloWuenne FloWuenne FloWuenne approved these changes

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@kbestak @FloWuenne