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Fgbio tmpdir modification #1890
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Can you also update the callmolecularconsensusreads to use the tmp dir and sortsam to the newest container + tmpdir? |
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
@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
approved these changes
Jul 15, 2022
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This PR changes the tmpdir definition in the fgbio modules to be equal to GATK, it also fixes the umi snappy error discussed here.
versions.yml
file.label
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