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This PR includes three files:
The Cromwell configuration we are currently using on DISCOVERY. It assumes a few things:
.SIFimage files on a shared disk locationorg/image:versiontoorg_image_version.sifto make them safe as filenames/projects/beyond_binding/cromwell_immuno_test/shared-sif-images/currently. I don't know if we'll want to make that parametrizable going forward.A new version of
runCromwellWDL.shmodified to handle the differences in the cluster environment from our compute1 or GCP environments.A concrete example of the command I ran in order to get a successful run of
immuno.wdlon the JHU cluster with the HCC1395 test data