We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
Specify number of cores for each task in LSF
I'm using WDL with a LSF backend. Right now I'm running the whole pipeline by doing "java -Dconfig.file=4core.conf -jar cromwell.jar run XXX.wdl XXX.json", where the "4core.conf" file specify that when WDL spawns a new process use 4 cores by doing "bsub -n 4".
My question is is there any way to set this "resource" request differently for different tasks? BWA MEM benefits alot from large number of cores, but my other tasks don't require nearly as much resources, however since the cromwell config file is invoked on the workflow level I cannot currently do that.