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Add module to fetch SDRF files from PRIDE Archive#11513

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jonasscheid merged 8 commits intonf-core:masterfrom
jonasscheid:pridepy-fetch-sdrf
May 7, 2026
Merged

Add module to fetch SDRF files from PRIDE Archive#11513
jonasscheid merged 8 commits intonf-core:masterfrom
jonasscheid:pridepy-fetch-sdrf

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@jonasscheid jonasscheid commented May 4, 2026

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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda

Notes

Version is currently captured via python -c "from importlib.metadata import version; ..." because the bundled pridepy 0.0.15 CLI does not expose a --version flag. Upstream PR PRIDE-Archive/pridepy#96 adds --version and has been merged; once a new pridepy release is published on bioconda, version parsing in this module will be simplified to pridepy --version in a follow-up.

@jonasscheid jonasscheid changed the title feat(pridepy/fetchsdrf): add module to fetch SDRF files from PRIDE Archive Add module to fetch SDRF files from PRIDE Archive May 4, 2026
@jonasscheid jonasscheid mentioned this pull request May 4, 2026
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@nf-core-bot fix linting

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@famosab famosab left a comment

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Nice work, i added a few suggestions feel free to do that or just merge :)

Comment thread modules/nf-core/pridepy/fetchsdrf/tests/main.nf.test Outdated
Comment thread modules/nf-core/pridepy/fetchsdrf/tests/main.nf.test Outdated
Comment thread modules/nf-core/pridepy/fetchsdrf/main.nf
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jonasscheid commented May 7, 2026

Thanks @famosab! Lint failing due to #11543

Still waiting until that is merged

@jonasscheid jonasscheid added this pull request to the merge queue May 7, 2026
Merged via the queue into nf-core:master with commit 8fd2462 May 7, 2026
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@jonasscheid jonasscheid deleted the pridepy-fetch-sdrf branch May 7, 2026 16:47
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3 participants