As of May 19, 2025, Cromwell uses Google Batch as it default API. Users can optionally move back to the Lifesciences API using Workspace Settings. Google is deprecating Lifesciences July 1.
What we're solving
Our WDL execution engine, Cromwell, currently leverages the Cloud Life Sciences API when launching workflows in Terra. Google is replacing Cloud Life Sciences with a next-generation API named GCP Batch (learn more). We have been updating Cromwell to work with the new API and are now testing it in Terra.
Migrating to Batch keeps Cromwell and Terra current with the latest improvements from GCP. We will release Cromwell on Google Batch iteratively, leveraging feedback from our community on the most important use cases.
Our release plan
Late March - Public Preview, Users can opt for any workspace to use the Cromwell on Batch API; as well as turn off Batch and return to using PAPI/Lifesciences.
May 19 - General Availability: All user workspaces are migrated to Batch API. For two weeks after this migration, users can optionally move back to the Lifesciences API if an issue arises.
July 1 - Life Sciences API support is no longer available on Terra.
Try it out
Go to the workspace where you would like to turn on the Batch API. In the upper right-hand corner of the workspace, click Settings, and Workspace Settings will pop up. Next to Run Workflows on GCP Batch slide the toggle to green and click Save at the bottom right.
If you would like for the workspace to go back to using Life Sciences, you can slide the same toggle back to grey and hit Save.
Current known changes to the user experience
- We are actively working on improving the troubleshooting journey, including easier to find and understand error messages.
- Google Batch’s troubleshooting documentation is a great resource for interpreting error codes (e.g. Batch Error 50001 is a VM preemption). Note: These are analogous to the PAPI error codes that you may be familiar with.
- For jobs run on Batch, clicking the compute details icon in Job Manager will now open the job details in the Google Batch Jobs UI in a new tab, as compared to LifeSciences jobs which opens a pop-up with the details in Job Manager itself.
- Previously, we reported that WDLs that reference `/cromwell_root` are incompatible with Google Batch. We now provide a symlink so that WDLs with this logic will work with Cromwell on Batch.
Known Issues
- We are aware of a transient issue where a task might fail with below error and are working on fixing this. But in the meantime relaunching the workflow with call caching enabled should fix the issue.
io.grpc.StatusRuntimeException: CANCELLED: checking service account permission
How to give us feedback
If you experience any issues or have feedback, please submit a support ticket by emailing support@terra.bio and including “Cromwell on Batch API” in the title.
