I am trying to run the CNV pipeline as a snakemake workflow on a cluster, but DetermineGermlineContigPloidy and GermlineCNVCaller keep garbing all available cores.
XX:ParallelGCThreads=1 does nothing and --disableSpark does not exist. Even cpulimit seems unable to limit cores. I am guessing that the problem lies with the child python processes. Is there a way to limit them?
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