Native Pythonic generator for CWL processes (CLIs & workflows)
Michael R. Crusoe edited this page Nov 8, 2016
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6 revisions
Proposal by Niels Drost & Michael R. Crusoe:
Python API to generate Python objects that wrap a CWL Process (a CommandLineTool, Workflow, or ExpressionTool)
Can be used to configure and run that Process in a Pythonic way
Useful in Jupyter Notebooks
A notebook that intersperses running these CWL Processes with their own computation could be exported into a pure CWL workflow with the in between steps turned into Python scripts (wrapped in a CWL CommandLineTool).
helloworld = cwlWrap("helloworld.cwl")
result = helloworld(name="Fred")
print result["greeting"]Hello, Fred!
import cwltool.factory
f = cwltool.factory.Factory()
echo = f.make("v1.0/v1.0/echo-tool.cwl")
out = echo(in="foo")