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Bump sentieon modules - #12983

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bump-sentieon
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bagnacan wants to merge 28 commits into
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bump-sentieon

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@bagnacan

@bagnacan bagnacan commented Sep 16, 2026

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This PR updates all sentieon modules to version 202503.03.
Note:

  • In some cases, the docker images have been replaced not just to reflect the sentieon 202503.03 version update, but also to include the full list of software packages specified by the environment.yml (where these updates took place, it was often the case that tests would pass using the docker profile and fail when using singularity profile).
  • In sentieon/rsemcalculateexpression, the linter raises an Invalid 'meta' keys detected: meta.strandedness error. I tried to overcome this issue by making strandedness an optional input value channel, and updated the tests accordingly; however, this adjustment broke a subworkflow that leverages on sentieon/rsemcalculateexpression. After asking for suggestions, I rolled-back the changes and left strandedness a meta attribute.
  • Even though both sentieon/rsemcalculateexpression's docker and singularity containers are built using the same environment.yml definition, sentieon/rsemcalculateexpression's tests remain flaky, with docker/conda profile tests producing a different snapshot (see here) than the one produced by the singularity profile (see here).

PR checklist

  • This comment contains a description of changes (with reason).
  • If necessary, include test data in your PR.
  • 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

@nf-core-bot

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@nf-core-bot fix linting pretty please 🙏

@nf-core-bot

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@nf-core-bot fix linting

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