Fix number of cpus for modules with piped tools #499
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ewels
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May 17, 2021
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LGTM 👌 Just need to fix the tests..
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These are the infamous |
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Sorry for resurrecting this thread four months after it was closed, but I wonder if splitting by 2 affects the performance of the aligner a bit. Looks like when we have a piped command, its almost always an aligner paired with samtools view, and samtools view is not a resource intensive process. In that case, the aligner should be getting more resources instead of samtools, right? What do you guys think? |
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Split the number of CPUs in modules with two tools in a piped command and each of them with an explicit declaration of the CPUs to be used. See #498
PR checklist
Closes #498
PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wdPROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wdPROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd