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Add nf-test to pipeline template CI workflow #2881

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@adamrtalbot adamrtalbot commented Mar 19, 2024

Will close #2854

Replaces CI workflow with nf-test version.

Changes:

  • Uses a Python script to find changed files between PR branch and base.
  • Flags any nf-test files present
  • Adds 'special' cases such as pipeline level tests
  • Identifies any dependencies of changed tests
  • Returns as list of nf-test files to run
  • Runs nf-test as a matrix over those files
  • Confirm pass based on results of previous

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

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@nf-core-bot changelog

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@mashehu mashehu left a comment

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first, we need docs on how to write nf-test for pipelines

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first, we need docs on how to write nf-test for pipelines

And I think this would make more sense with a test added to the pipeline.

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We should also add nf-test to the pipieline template, the current template doesn't have them, so this won't work with most of the pipelines which don't have nf-test.

adamrtalbot added a commit to adamrtalbot/tools that referenced this pull request May 22, 2024
tags.yml is no longer needed with newer testing workflows. This PR removes the file from the module and subworkflow templates and updates the linting tests to reflect this.

Related to nf-core#2881
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4 participants