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.
How to control paralleling among nodes or in the same node?
Recently I am using GATK to call variants on re-sequencing data. All of calculations are done on a HPC runing Slurm on it. Each node have same number of CPUs and is exclusive. To speed up, I have been split FASTQ file of one sample into several parts and running parallele until variants calling. There are tasks such as trimmomatic that can not use multi-threads. In this situation I want to run tasks on diffencet parts in parallel in one node. There are other tasks such as HaplotypeCaller that can run parallel (-nct). So I want to run a part on one node using all CPUs(-nct). My question is how to control the parallel pattern using WDL and Cromwell?