I feel like I’m missing something obvious.
I am using cromwell to run cwl on an HPC cluster. The cluster uses slurm for job management. I want to be able to adjust the resources requested of slurm, dependent on what different tasks within the cwl workflow. i.e. I would like to request more memory, time and cpus when running bwa than when I am running a samtools sort. To me, this seems like a fairly basic requirement, there must be documentation around this somewhere surely?
Cromwell allows you to specify a config file that overrules the defaults, creating the slurm job file. I can’t find anything that tells me how to get information from the cwl file, to that config file though, which means that at the moment, I can only specify a single set of slurm job requirements with no ability to customize.
I thought it might have involved runtime variables - but a) I don’t appear to be able to pass them to the cromwell config file and b) I can’t see a way to pass variables that I define, like how much time I want the job to reserve.