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Snapshot all files (content or file name when not stable) #1360

Merged
merged 44 commits into from
Aug 27, 2024
Merged

Snapshot all files (content or file name when not stable) #1360

merged 44 commits into from
Aug 27, 2024

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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 marked this pull request as draft August 21, 2024 17:54
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github-actions bot commented Aug 21, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e4cfa09

+| ✅ 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 2024-08-26 18:05:44

@maxulysse maxulysse mentioned this pull request Aug 22, 2024
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@maxulysse maxulysse changed the title snapshot all files contents by default Snapshot all files (content or file name when not stable) Aug 22, 2024
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@nf-core-bot fix linting pretty please 🙏

@maxulysse maxulysse marked this pull request as ready for review August 26, 2024 15:40
pinin4fjords
pinin4fjords approved these changes Aug 27, 2024
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@pinin4fjords pinin4fjords left a comment

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To your point on Slack we probably should just be emitting everything from workflows/rnaseq/main.nf and testing from there.

But I think this is a good enough place to start- lots of work!

@maxulysse maxulysse merged commit 8679eda into nf-core:dev Aug 27, 2024
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

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@maxulysse @pinin4fjords