We've moved!
For WDL questions, see the WDL specification and WDL docs.
For Cromwell questions, see the Cromwell docs and please post any issues on Github.

Can I specify additional parameters for the Cromwell submit configuration based on each task?

mmahmmah Member, Broadie ✭✭

I am trying to run Cromwell on an LSF cluster. I have uncommented the LSF portion of the reference.conf file and set the default backend to LSF.

The example configuration for the submit is:
submit = "bsub -J ${job_name} -cwd ${cwd} -o ${out} -e ${err} /bin/bash ${script}"

I am encountering a problem because my LSF has a mandatory bsub argument for specifying a run time cutoff for each job '-W [max runtime]'.

I can easily insert a -W flag and hard-coded run time ceiling, but this will be for all jobs. Is there a way for me to introduce a new variable in the submit configuration that can reference a task property for run time?

Best Answer


Sign In or Register to comment.