However, this would always submit the scripts with a fixed number of CPUs and time.
Not sure if this can be changed on a step-by-step basis, based on the workflow somehow (like with Nextflow).
The config file can be used with the pipeline by running it as:
cromwell -Dconfig.file=csd3.conf run helloworld.wdl
The Broad Institute workflow engine
cromwell
can be useful to running GATK workflows (written in WDL language).Resources for this:
Some attempt to run this on CSD3. I have set the following config file:
However, this would always submit the scripts with a fixed number of CPUs and time. Not sure if this can be changed on a step-by-step basis, based on the workflow somehow (like with Nextflow).
The config file can be used with the pipeline by running it as: