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This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions 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?