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Integrated nf-test into pipeline CI #71

Merged
merged 5 commits into from
Oct 22, 2024
Merged

Integrated nf-test into pipeline CI #71

merged 5 commits into from
Oct 22, 2024

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GallVp
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@GallVp GallVp commented Oct 21, 2024

PR checklist

  • Integrated nf-test into pipeline CI
  • 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
  • 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 Oct 21, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 97ed70e

+| ✅ 101 tests passed       |+
#| ❔  18 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: assets/nf-core-genepal_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genepal_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genepal_logo_dark.png
  • nextflow_config - nextflow_config
  • files_unchanged - File does not exist: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File does not exist: assets/nf-core-genepal_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genepal_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genepal_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/genepal/genepal/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-22 03:58:35

@GallVp GallVp merged commit 35f6d64 into dev Oct 22, 2024
61 checks passed
@GallVp GallVp deleted the add/nftest branch October 22, 2024 06:38
@GallVp GallVp linked an issue Oct 24, 2024 that may be closed by this pull request
Use nf-test for pipeline level tests #68
Open
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Use nf-test for pipeline level tests
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