We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.
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?