broadinstitute / PANOPLY

Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)
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Issue separate normalize #26

Closed mmaynard-source closed 3 years ago

mmaynard-source commented 3 years ago

Updated panoply_normalize_ms_data and panoply_normalize_ms_data_report to be a workflow separate from panoply_main. Normalize workflow was added to panoply_unified_workflow and outputs were channeled to appropriate modules requiring normalized ome input gct files.

Various default parameters were updated for modules, particularly those needing runtime parameter changes such as memory.

In panoply_unified_workflow, the Blacksheep workflow will now run on cna data when provided as pipeline input.