Update: July 26, 2019
This section of the forum is no longer actively monitored. We are working on a support migration plan that we will share here shortly. Apologies for this inconvenience.

Cromwell Filesystem option


We're planning to migrate our pipelines to WDL/CWL ran by a Cromwell server.
As small situation sketch:

  • Pipeline in WDL/CWL -> submit to Cromwell server
  • Cromwell submits jobs to an on-site Slurm cluster. Data is hosted on a local S3 server.

My question now, is there a way to add S3 as a filesystem? (NOT as batch execution)
We're also looking into setting up a DRS service, based on the GA4GH scheme. Are there plans to update the DRS docs for cromwell?


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