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Implement nf-test on Pipeline level and Github CI #118

Merged
merged 20 commits into from
Jun 10, 2024
Merged

Implement nf-test on Pipeline level and Github CI #118

merged 20 commits into from
Jun 10, 2024

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tillenglert
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@tillenglert tillenglert commented Apr 19, 2024 •
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PR will implement nf-test on Pipeline level and mimics the previous CI tests (Only checking for pipeline success. A second PR will then add assertions to each test to check results of the pipeline runs.

Additional tests (needing ncbi_key and ncbi_email) are tested on the synced PR: #119

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 (nf-test test main.nf.test -profile test,docker).
  • 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).

@tillenglert tillenglert changed the title Change CI to include nf-test (no ncbi credentials) Implement nf-test on Pipeline level and Github CI Apr 19, 2024
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github-actions bot commented Apr 19, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 879ee06

+| ✅ 192 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   2 tests had warnings |!
-| ❌   5 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • base_config - conf/base.config contains withName:CUSTOM_DUMPSOFTWAREVERSIONS, but the corresponding process is not present in any of the Nextflow scripts.
  • modules_config - conf/modules.config contains withName:CUSTOM_DUMPSOFTWAREVERSIONS, but the corresponding process is not present in any of the Nextflow scripts.

❗ 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 2.14.0
  • Run at 2024-05-08 15:45:22

@tillenglert tillenglert force-pushed the nf-test_implementation branch from 1749fb4 to 383e49a Compare April 24, 2024 12:16
@tillenglert tillenglert force-pushed the nf-test_implementation branch from 618a28b to 643061a Compare April 26, 2024 08:09
@tillenglert tillenglert marked this pull request as ready for review April 26, 2024 12:17
@tillenglert tillenglert requested a review from skrakau April 26, 2024 12:17
skrakau
skrakau reviewed May 8, 2024
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skrakau approved these changes May 31, 2024
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LGTM! (without being the nf-test expert ;) )

@tillenglert tillenglert merged commit 6db5834 into nf-core:dev Jun 10, 2024
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@tillenglert tillenglert deleted the nf-test_implementation branch June 25, 2024 07:33
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@skrakau skrakau skrakau approved these changes

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