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Add instructions for canceling runs #112

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jashapiro opened this issue Jan 14, 2025 · 1 comment · Fixed by #117
Closed

Add instructions for canceling runs #112

jashapiro opened this issue Jan 14, 2025 · 1 comment · Fixed by #117
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@jashapiro
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The internal readme does not describe how to cancel a run in progress, which is sometimes desirable. Doing so requires access to the workloads account, and a few unusual steps to login to the running EC2 instance.

The short version is:

  • From the workloads account, go to EC2 and locate the Nextflow-workload instance.
  • Click the "Connect" button, then choose the "Session Manager" tab and then click "Connect"
  • In the terminal that opens, enter teh following commands
    • sudo su ec2-user
    • tmux a

If there is an active run, you should then see the Nextflow run in progress (If there is not, you will get a "no sessions" message). To cancel the run, enter control-c.

If you wish to exit without canceling the run, you can simply close the tab, or press control-b followed by d to detach from the tmux session.

Other instructions to include might be where the active log file is for monitoring. I think it should be at /opt/nextflow/.nextflow.log

@jashapiro
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It might make sense to bundle this with better instructions for local workflow testing. See #113 (review) for some thoughts (not quite tested) on that front.

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