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nf-test assertions #128

Merged
merged 5 commits into from
Aug 6, 2024
Merged

nf-test assertions #128

merged 5 commits into from
Aug 6, 2024

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tillenglert
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@tillenglert tillenglert commented Jul 18, 2024 •
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This PR includes the nf-test assertions for the latest refactoring (#127). The checks will fail until the previous PR is merged.

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/metapep 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 Jul 18, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 707375c

+| ✅ 196 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-06 11:16:42

@tillenglert tillenglert mentioned this pull request Jul 18, 2024
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d4straub
d4straub approved these changes Aug 6, 2024
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Looks fine to me.
Some blank lines could be removed I think, but not important.
d41d8cd98f00b204e9800998ecf8427e, which is an empty string, appears for prediction_warnings.log, but that seems fine. (7029066c27ac6f5ef18d660d5741979a, an empty compressed file is not present)

tests/pipeline/test_all.nf.test Show resolved Hide resolved
@tillenglert
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Thanks @d4straub ! The empty md5sum of the *.log is to check if there will be warnings if something has actually changed. I will remove the empty files, I split the blocks into the directories within the results dir, but sure it is just many blank lines. I will push a commit soon and merge afterwards 🙂

@tillenglert tillenglert merged commit 3b46b3c into nf-core:dev Aug 6, 2024
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@tillenglert tillenglert mentioned this pull request Aug 6, 2024
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@tillenglert tillenglert deleted the nf-test_assertions_new branch August 6, 2024 12:28
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@d4straub d4straub d4straub approved these changes

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