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.

Loading modules for specific tasks


I'm running a wdl workflow using cromwell 39 on a slurm cluster, and was wondering if there is a way load environment modules for tasks without having to include the module load <module name> line to the command part of each task (because I'm also running the pipeline in AWS, where I wouldn't have access to environment modules).
I tried to add the load command as part of the submit command in my configuration file - but to no avail (understandably). Is there a way around that obviates touching the workflow script itself?

Thank you,

Sign In or Register to comment.