Cancelling a workflow post invocation


We are using a local instance (v22.05) . We have a workflow that spawns thousands of jobs. I was wondering if there is a way to cancel a workflow (e.g a user realizes a mistake) post invocation which will delete all the running/pending jobs pertaining to the invocation. Manually deleting jobs gets cumbersome and confusing especially because purged datasets are still visible in history.


Hi @microfuge

You can quit out for a very short window on the invocation view. After that, the processes are scheduled and I don’t think there is an “undo” function to recall those.

Technically, an administrator on the backend could look up that invocation, then any associated processes, and do what they want … but there isn’t a button for a user in the application for the same that I know of.

What you could try instead:

  1. Create a history that contains all of the workflows inputs.
  2. Execute the workflow while that “input” history is active but send the output to a new history.
  3. If something goes wrong, purge that new history.
  4. Your original inputs will still be in the original history, so you can repeat this.
  5. The jobs already sent out as scheduled will error when that new history isn’t available, and abort the remainder of the workflow.

This seems like a good feature request! It wouldn’t help with older releases, but could improve future versions. Please consider creating the request here if that interests you: Issues · galaxyproject/galaxy · GitHub

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Hi Jennifer @jennaj

Thanks so much. Special thanks for the “cancel scheduling” button (I don’t know how I missed this for so long). The new history trick is great and works.

I agree that this is a good feature to have. The link to the issue is [Feature request] Cancelling a workflow post invocation · Issue #16781 · galaxyproject/galaxy · GitHub
Thanks Again!

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