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Enhancement: Updated nf-tests. #107

Merged
merged 2 commits into from
Mar 5, 2025
Merged

Enhancement: Updated nf-tests. #107

merged 2 commits into from
Mar 5, 2025
+450 −110

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FloWuenne
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Description

This PR updates all nf-tests to use nft-utils as suggested by @maxulysse in here: #105 (comment) . Nf-tests now use nft-utils to test all stable file names and paths.

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).

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github-actions bot commented Mar 5, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5a47e10

+| ✅ 223 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_unchanged - File ignored due to lint config: assets/nf-core-molkart_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-molkart_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-molkart_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-03-05 18:06:21

kbestak
kbestak approved these changes Mar 5, 2025
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Thanks so much for adding this!
Looks great to me! 🚀

@kbestak kbestak linked an issue Mar 5, 2025 that may be closed by this pull request
Fully move to nf-test #77
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@FloWuenne
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Closes #77 !

@FloWuenne FloWuenne merged commit c6e41ab into dev Mar 5, 2025
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@FloWuenne FloWuenne deleted the update_nftests_nft-utils branch March 5, 2025 20:43
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@kbestak kbestak kbestak approved these changes

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Fully move to nf-test
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@FloWuenne @kbestak