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Migrate pytest aligner and pipeline default tests to nf-test #1678

Merged
merged 25 commits into from
Oct 23, 2024
Merged

Migrate pytest aligner and pipeline default tests to nf-test #1678

merged 25 commits into from
Oct 23, 2024

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maxulysse
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Replace #1675

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/sarek 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 changed the base branch from master to dev October 8, 2024 05:41
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github-actions bot commented Oct 8, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fb9b6ee

+| ✅ 214 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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 base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-23 10:25:17

@maxulysse maxulysse changed the title Migrate pytest aligner tests to nf-test Migrate pytest aligner and pipeline default tests to nf-test Oct 8, 2024
@nf-core nf-core deleted a comment from github-actions bot Oct 8, 2024
nvnieuwk
nvnieuwk previously approved these changes Oct 8, 2024
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This looks so beautiful!

@maxulysse maxulysse mentioned this pull request Oct 8, 2024
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@fellen31 fellen31 mentioned this pull request Oct 8, 2024
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@maxulysse maxulysse mentioned this pull request Oct 11, 2024
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maxulysse
maxulysse commented Oct 23, 2024
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@maxulysse
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THANK YOU SO MUCH @FriederikeHanssen

@maxulysse maxulysse merged commit 100258d into nf-core:dev Oct 23, 2024
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@maxulysse maxulysse deleted the nft-utils-0-0-3 branch October 23, 2024 10:43
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@nvnieuwk nvnieuwk nvnieuwk left review comments

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@maxulysse @nf-core-bot @FriederikeHanssen @nvnieuwk