parse commandline flags/options when validating workflow

[sphemakh]

I have a workflow that uses a cwl-extension which is not part of the standard. I'd like to be able to parse the "--enable-ext" flag to cwltool when validating the workflow.

[jvdzwaan]

It is not entirely clear to me what enable_ext does. I made a branch (enable_ext) which uses some code copied from cwltool to load/validate workflows using --enable-ext (or my best first guess at doing so). Can you test this?

To save using enable_ext do:

wf.save('workflow.cwl', enable_ext=True)

Also, I would be grateful if you can provide me with an example for testing purposes.

[jvdzwaan]

Example of CommandLineTool that needs enable_ext: https://github.com/apertif/apercal/blob/cwl/cwl/steps/preflag.cwl