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common-workflow-language / cwltool

Common Workflow Language reference implementation
https://cwltool.readthedocs.io/
Apache License 2.0
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document troubleshooting techniques #1434

Open srp33 opened 3 years ago

srp33 commented 3 years ago

Expected Behavior

When a permanentFail occurs, stdout/stderr outputs should be preserved.

Actual Behavior

When a permanentFail occurs, stdout/stderr outputs are not preserved.

Working example

An example that illustrates this problem is described here: https://cwl.discourse.group/t/forcing-stdout-and-stderr-to-be-written-when-a-tool-fails/342

If it would be helpful, I can copy the details here from there.

My Environment

mr-c commented 3 years ago

@srp33 As a workaround for now, if you use cwltool --cachedir some/path my_workflow.cwl my_inputs.yml then all intermediate outputs are preserved inside the --cachedir directory

kannon92 commented 2 years ago

Hey, as a side effect of my addition of real time logs, you can actually use that argument to log stdout/stderr of a workflow step to a local filesystem.

The PR was here:

https://github.com/common-workflow-language/cwltool/pull/1600

mr-c commented 2 years ago

Thanks @kannon92

Maybe we should create a new documentation page with troubleshooting tips? We can include your log dir feature and my workaround