I'm trying to build a workflow with a step that doesn't take any input:
The workflow fails to validate with this error:
/home/psafont/.virtualenvs/cwl/bin/cwl-runner 1.0.20161207161158
Resolved 'textures.cwl' to 'file:///home/psafont/dev/stellaris-emblem-lab/textures/scripts/textures.cwl'
Tool definition failed validation:
Validation error in object file:///home/psafont/dev/stellaris-emblem-lab/textures/scripts/textures.cwl
Could not validate `Workflow` because
Workflow record could not validate field `steps` because
the value `[{'id': u'file:///home/psafont/dev/stellaris-emblem-lab/textures/scripts/textures.cwl#gradients',
'out': [u'file:///home/psafont/dev/stellaris-emblem-lab/text[...]`
is not a valid type in the union, expected one of:
- array of <WorkflowStep>, but
At position 0
missing required field `in`
This is the workflow:
cwlVersion: v1.0
doc: Create emblem textures
class: Workflow
inputs:
outlines: File[]
outputs:
texture_small:
type: File
outputSource: textures/small
outputBinding:
outputEval: texture/$(inputs.outline.nameroot).dds
steps:
gradients:
id: gradients
run: tools/gradients_gen.cwl
out: [fill_gradient, highlight_gradient]
textures:
id: textures
run: texture_emblem.cwl
requirements: ScatterfeatureRequirement
scatter: outline
in:
outline: outlines
fill_gradient: gradients/fill_gradient
highlight_gradient: gradients/highlight_gradient
out: [small]
I'd like to know if the 'in' parameter is not-so-optional or there's something else I'm missing.
Note: I'm sure there are other mistakes in the workflow, but this is the error I'm encountering right now :)
•
written
by
unduthegun •
You need to provide an "in" section with an empty list. Also "id: gradients" is redundant:
gradients:
run: tools/gradients_gen.cwl
in: []
out: [fill_gradient, highlight_gradient]
However you're right, as a general rule, fields which can accept empty lists should be optional.
I see, I found it confusing because I understood from the documentation that the field is optional.
From Fields in Subworkflows in http://www.commonwl.org/v1.0/Workflow.html#WorkflowStep :
field: in; type: [...]; required: Optional; description: [...]
That's odd, there is an error with the website generation; that field is indeed required in v1.0. [Peter, looks like a bad version of schema salad?]
The website has been fixed -- thank you for bringing that to our attention. I agree with Peter that fields which can accept empty lists should be optional.
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