Hi, this is a cwl syntax question. I have a simple python script that creates two files:
with open("A.txt", "w") as f: f.write("lpha") with open("x/x/B.txt", "w") as f: f.write("eta")
And I want to run this with cwl.
The first file creation runs and works fine, because it deposits the file in the working directory. The second does not work because the folders "x/x" seem to not be recreated in the temporary folder that cwl uses. I've tried to specify these folders as inputs (which I think is correct?) with the following attempt:
cwlVersion: v1.0 class: CommandLineTool baseCommand: python inputs: - id: xdir type: Directory - id: src type: File inputBinding: position: 1 outputs: - id: A type: File outputBinding: glob: "A.txt"
Here is the .yml:
src: class: File path: makefile.py xdir: class: Directory path: x/x
How should I write these so that this will run? Thanks!