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add stub for local modules #1331

Merged
merged 5 commits into from
Jul 2, 2024
Merged

add stub for local modules #1331

merged 5 commits into from
Jul 2, 2024
+557 −54

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maxulysse
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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/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).

@maxulysse maxulysse mentioned this pull request Jun 21, 2024
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github-actions bot commented Jun 21, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7e9077e

+| ✅ 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 2024-07-02 14:54:30

@maxulysse maxulysse marked this pull request as ready for review June 21, 2024 10:12
@FriederikeHanssen
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CHANGELOG is missing

maxulysse
maxulysse commented Jul 2, 2024
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modules/local/deseq2_qc/main.nf
Comment on lines +76 to +79
for i in `head $counts -n 1 | cut -f3-`;
do
touch size_factors/\${i}.size_factors.RData
done
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I'm quite proud of that one

@maxulysse maxulysse enabled auto-merge July 2, 2024 15:03
@maxulysse maxulysse merged commit b901cbe into nf-core:dev Jul 2, 2024
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@maxulysse maxulysse mentioned this pull request Jul 4, 2024
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@adamrtalbot adamrtalbot adamrtalbot approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen @adamrtalbot