Update HaplotypeCaller_GATK4_VCF to use MEM_SIZE and MEM_UNIT #1448
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Description
The task
HaplotypeCaller_GATK4_VCF
had a "Note: In the future this should be done using Cromwell's ${MEM_SIZE} and ${MEM_UNIT} environment variables". This pull request replaces the note with code that uses those environment variables.Before this change, when this WDL runs on a machine with shared memory, such as on a high-performance computing (HPC) cluster or laptop, the command
free
returns the full memory of the machine. Instead of the amount of memory assigned to the job should be used. To work around this issue, the MEM_SIZE and MEM_UNIT environment variables are now used when present.Note to anyone else trying to use this workflow on their HPC/laptop: as of December 2024 you must run a fork of Cromwell that incorporates MEM_SIZE and MEM_UNIT in your backend, otherwise
free
will still be used incorrectly. For more info on memory and memory-retry issues and Cromwell see these years-old PRs, especially 6766:Checklist
If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP team by tagging @broadinstitute/warp-admins in a comment on this PR.