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Fgbio tmpdir modification#1890

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FriederikeHanssen merged 14 commits intonf-core:masterfrom
WackerO:fgbio_error
Jul 15, 2022
Merged

Fgbio tmpdir modification#1890
FriederikeHanssen merged 14 commits intonf-core:masterfrom
WackerO:fgbio_error

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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!
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    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
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Comment thread modules/fgbio/groupreadsbyumi/main.nf Outdated
Comment thread modules/fgbio/fastqtobam/main.nf Outdated
@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>
Comment thread modules/fgbio/sortbam/main.nf Outdated
@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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