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mskcc / pluto-cwl

CWL workflows for helix filter scripts
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Feature/msi #34

Closed timosong closed 3 years ago

timosong commented 3 years ago

Adding MSI feature

stevekm commented 3 years ago

do we need to have all of the optional args for MSI sensor in the CWL? Aren't we only using a couple of them?

can we rename the CWL input args to human-readable things like input_file and output_file?

What are the downstream steps to get the MSI score merged into the pipeline output? And where does this get run inside workflow_with_facets.cwl?

stevekm commented 3 years ago

can you merge the latest dev into this?

stevekm commented 3 years ago

make sure we change merge-tables.cwl to a version release of the Docker container