Making memory an optional parameter for ValidateVcf task #1144
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requested review from
fleharty,
gbggrant,
kachulis and
samuelklee
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@meganshand we'll need to bump the pipeline version numbers in the documentation but I can take care of that |
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@kayleemathews Thanks, I didn't realize I needed to change the versions elsewhere. I'll try to follow how you fix it to update those next time. |
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@meganshand No worries! I'm often the one who goes in to update the versions listed in the docs. Sometimes the changes being made require bigger changes to the documentation, but these ones should be pretty simple :) |
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Remember to squash merge! |
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Remember to squash merge! |
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Remember to squash merge! |
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passing scientific JG test: https://gotc-jenkins.dsp-techops.broadinstitute.org/job/warp-workflow-tests/59328/console passing check fp test: https://gotc-jenkins.dsp-techops.broadinstitute.org/job/warp-workflow-tests/59349/console |
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When running the
ReblockGvcfspipeline without acalling_interval_list, the validation occurs over the intervals from the input (unreblocked) GVCF. In this case ValidateVariants requires much more memory. This argument will allow users to be able to adjust the memory to that task as needed if they don't provide the optionalcalling_interval_list. See also this GATK issue: broadinstitute/gatk#8608For typical WGS GVCFs (around 4Gb inputs) using 32 Gb of memory allowed the task to pass (setting
machine_mem_mb=32000).