Have Cromwell option ContinueWhilePossible exposed to user.

Post author
Steve Huang

Hi,

In summary, we are asking for the Cromwell option to be exposed on Terra

"workflow_failure_mode": "ContinueWhilePossible"

Useful scenario:

Say a small/trivial task failed in a big pipeline, but that trivial task started hours after a more intensive task had started. And unfortunately the intensive task was preempted. Without the choice of choosing to continue-when-possible, the task will NOT be re-tried, hence I am left with an unintuive behavior: I see a workflow failed seemingly due to PAPI 14, that is never re-tried.

There are times where I'd hope the intensive task to be retried even though the overall execution is doomed, but I can fix whatever bug in the trivial task later and make use of call-caching to speed things up.

Cromwell currently supports this via 

https://cromwell.readthedocs.io/en/stable/wf_options/Overview/

But on Terra, we don't have that option exposed to us.

This is related to another ticket from a year ago

https://support.terra.bio/hc/en-us/community/posts/360074147472-ContinueWhilePossible-not-default-?input_string=Have%20ContinueWhilePossible

 

Thanks!

Steve

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