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broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing
BSD 3-Clause "New" or "Revised" License
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Make the Cromwell root config in the MELT workflow portable #602

Closed VJalili closed 9 months ago

VJalili commented 10 months ago

The root directory of the VM started by Cromwell to run a task is a Cromwell instance configuration. The default value is set to /cromwell_root and /cromwell-executions on GCP and Azure, respectively.

MELT script takes the root directory as an input, and MELT's WDL hardcodes this input to /cromwell_root, which works as expected on GCP. However, the hardcoded value is not portable.

This PR extends the hardcoded value to the default Cromwell root directories to GCP and Azure, and uses $PWD (discussed in https://github.com/broadinstitute/gatk-sv/issues/365#issuecomment-1172809000) as a fallback option if the Cromwell root was set to a different value.

The changes are successfully tested on GCP and Azure. The GCP workflow id is: f450a355-031f-44fc-8289-d199d0fd93e8.

VJalili commented 9 months ago

Thank you, Mark! Setting to CROMWELL_ROOT="$PWD" would have been simpler; I tried it, but it fails on GCP on the Cromwell instances I used.