Open jfennick opened 1 year ago
This was fixed already in https://github.com/common-workflow-language/cwltool/pull/1813
Looks like I was one day too late! Thanks, I can confirm that with #1813 the first two examples are now fixed. However, I'm still getting the same errors for the second two examples.
cwltool --enable-dev --enable-ext pytoolgen_wrap.txt zing.txt
cwltool --enable-dev --enable-ext pytoolgen_wrap_runProcess.txt zing.txt
According to the ProcessGenerator documentation, https://github.com/common-workflow-language/cwltool/blob/main/docs/processgen.rst
However, it appears that the final output is the generated process itself (i.e. the output of the embedded script), rather than the output of the generated process.
It should be noted that the attached pytoolgen.txt explicitly contains
outputs: {}
, which is apparently ignored.Moreover, if any other top-level
outputs
are given (even constant literals) they are again ignored, along with the output of the generated process.The plot thickens if we try to wrap a ProcessGenerator in a single step workflow:
So it appears that the
outputs
are NOT being ignored w.r.t. a parent workflow. Moreover, if we explicitly shadow the (correct?) output, we get a different error:Expected Behavior
pytoolget.txt should return the output from the generated process, not the generated process itself. pytoolgen_myoutput.txt should also return "myoutput"
pytoolgen_wrap.txt and pytoolgen_wrap_runProcess.txt should return the same output as the underlying ProcessGenerator (whatever that might be).
Actual Behavior
In both cases, the generated process itself is returned, not its output.
pytoolgen_wrap.txt and pytoolgen_wrap_runProcess.txt return the above errors.
Workflow Code
pytoolgen_runProcess.txt pytoolgen_myoutput.txt pytoolgen_wrap_runProcess.txt pytoolgen.txt pytoolgen_wrap.txt zing.txt
Full Traceback
See above
Your Environment