document troubleshooting techniques

[srp33]

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

• cwltool version:
  3.0.20201203182617 (Mac OS)

[mr-c]

@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]

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:

#1600

[mr-c]

Thanks @kannon92

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