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@Aratz Aratz commented Nov 7, 2025

This is the second attempt to make it easier and faster to use the tests when developing the pipeline (first attempt was PR #161)

This PR does the following:

  • Merge all mpx pipeline tests, and all pna pipeline tests
  • Execute the experiment summary in test mode
  • Add missing stub tests for PNA modules
  • Snapshot only the file list and the version file, for all tests. Content validation is done internally in the pixelator tests
  • Add script to run the tests in parallel locally
  • Tag one test as smoke test for quick diagnostics and add a script to run it.

PR checklist

  • This comment contains a description of changes (with reason).
  • If necessary, also make a PR on the nf-core/pixelator branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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>).
  • CHANGELOG.md is updated.

@Aratz Aratz self-assigned this Nov 7, 2025
@Aratz Aratz marked this pull request as ready for review November 7, 2025 14:47
@Aratz Aratz requested a review from a team as a code owner November 7, 2025 14:47
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@fbdtemme fbdtemme left a comment

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Very nice!
Only thing I am unsure about is the test scripts. I have not really seen any custom scripts being used in other nf-core repos so maybe the core folks would have issues with that?

I would just leave those out.

@johandahlberg
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Maybe it is something to bring to the table and hear what the nf-core folks think about it? Since testing seems to be a pain point for main pipeline as I understand it.

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Aratz commented Nov 21, 2025

I can ask on slack and fix it in a new PR if I get any suggestions, thanks for the review!

@Aratz Aratz merged commit 28a603f into nf-core:dev Nov 21, 2025
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@Aratz Aratz mentioned this pull request Dec 11, 2025
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3 participants