For WDL questions, see the WDL specification and WDL docs.
For Cromwell questions, see the Cromwell docs and please post any issues 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?