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Set PYTHONHASHSEED for umitools dedup #1932

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Aug 31, 2022
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@SPPearce SPPearce commented Jul 28, 2022

The umi_tools dedup command is not currently deterministic, even if --random-seed is set, unless the PYTHONHASHSEED environment variable is also set. Detailed in CGATOxford/UMI-tools#440 and https://github.com/CGATOxford/UMI-tools/pull/470. Not fixed in the main umitools, so just explicitly export the environment variable here.

  • 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.
  • Emit the versions.yml file.
  • 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:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

@SPPearce SPPearce self-assigned this Jul 28, 2022
@SPPearce SPPearce added the bug Something isn't working label Jul 28, 2022
@SPPearce SPPearce requested a review from drpatelh July 28, 2022 13:45
@SPPearce SPPearce merged commit 9d48964 into nf-core:master Aug 31, 2022
@SPPearce SPPearce deleted the umitools2 branch August 31, 2022 13:06
matthdsm pushed a commit to matthdsm/nf-core-modules that referenced this pull request Sep 5, 2022
Set PYTHONHASHSEED

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
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