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Fgbio tmpdir modification #1890

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merged 14 commits into from
Jul 15, 2022
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WackerO
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@WackerO WackerO commented Jul 15, 2022

This PR changes the tmpdir definition in the fgbio modules to be equal to GATK, it also fixes the umi snappy error discussed 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

@FriederikeHanssen
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Can you also update the callmolecularconsensusreads to use the tmp dir and sortsam to the newest container + tmpdir?

WackerO and others added 4 commits July 15, 2022 10:51
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
@FriederikeHanssen
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@WackerO I think you might need to double check the tests that are run. When the module callmolecularconsensusreads is run, also the module sortsam is executed. Might be something about the tags

@FriederikeHanssen FriederikeHanssen merged commit 6720d88 into nf-core:master Jul 15, 2022
@WackerO WackerO deleted the fgbio_error branch July 15, 2022 09:22
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