For WDL questions, see the WDL specification and WDL docs.
For Cromwell questions, see the Cromwell docs and please post any issues 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?