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Cromwell is slow to submit jobs in large scatter on JES
Hi GATK team,
I'm running a WDL script on cromwell 34 against a JES backend. The WDL is pretty simple - I am filtering a list of VCF files against a BED file of sites I want to keep. The WDL looks like this: https://gist.github.com/weinstockj/30e0d99d11e9a2633cf7602b74cbf5fe
Cromwell is very slow to submit jobs. I am using a very large input TSV of VCFs (39K files). By slow, I mean I have submitted jobs to a beefy cromwell VM, and it takes over an hour for any JES jobs to spin up. I was previously running this workflow on cromwell 31, where I experienced this issue as well. I'm running Cromwell in server mode, and after workflow submission, it displays very little CPU activity. When running this workflow with a small number of VCF files (100 VCFs), I do not experience the slow job submission. Is there a way that I can re-structure the WDL to avoid the the slow job submission (beyond splitting up things into smaller batches)?