One thing I really like about CWL is the ability to load CWL files into a CommandLineTool or Workflow object after generating the classes using schema-salad-tool --codegen=python CommonWorkflowLanguage.yml > cwl_classes.py
. Is there a schema file that describes CWL inputs/job files similar to CommonWorkflowLanguage.yml? I have been working with these files as dicts, but would be super nice to be able to load them straight into a class object.
Thanks! I remember coming across this at some point now...
I am testing dnanexus/dxCompiler. And get this error? Is this something "CWL-like" I can fix or is it just something I cannot do until they reply to my issue.
Command:
java -jar dxCompiler-2.4.7.jar compile /Users/****/****/UKBB/analysis-workflows/definitions/pipelines/CH_exome_Final2.cwl -language CWL
Error: Custom types is "missing definition for schema"
I see that you've already opened an issue at that repo: https://github.com/dnanexus/dxCompiler/issues/149
That's probably the best place to ask, yes.
Does the CWL reference runner,
cwltool
, accept your inputs?