By default, Cromwell sets the Java temp directory to $HOME/.tmp. This memory has much slower read/write speeds than the $SCRATCH
directories. This will cause speed problems on any memory intensive programs (I originally encountered this issue with using
MarkDuplicates with Cromwell). Setting the Java temp directory to /tmp in the cromwell config file with the temporary-directory
setting seems to fix the slowdown. See my GATK forums question for more info here.