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mskcc / pluto-cwl

CWL workflows for helix filter scripts
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deprecate run.py script #77

Closed stevekm closed 2 years ago

stevekm commented 2 years ago

The run.py script and run-json.py scripts should be deprecated, along with the operator sections, in lieu of using the cwltool and Toil built-in CLI args to supply CWL inputs

Migrate the included CWL manual-run methods from these scripts over to the "run" scripts in the pluto subdir;

https://github.com/mskcc/pluto/blob/master/run-toil.sh https://github.com/mskcc/pluto/blob/master/run-cwltool.sh

These scripts do the same basic things as run.py but are not tied specifically to pluto-cwl CWL workflows.

stevekm commented 2 years ago

Note that we would still need a better method for creating workflow.cwl and workflow_with_facets.cwl inputs because of the use of arrays of files and other complicated data structure input types