CNV-freec and CNV-varscan pipelines not available

oicr-gsi / cbioportal_tools

tools for import of data and administration of the gsi cbioportal instance

GNU General Public License v3.0

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CNV-freec and CNV-varscan pipelines not available #28

Open lheisler opened 5 years ago

lheisler commented 5 years ago

There are pipeline scripts for these tools, but when i run i get a message saying that these are not available

ERROR:: The pipeline (CNV-freec) you have placed in the SEG file is not currently supported. Please use one of these ['CNVkit', 'Sequenza', 'HMMCopy']

This has to do with a check on the pipeline, with the acceptable values currently hardcoded. I have a separate ticket open to address this hardcoding.

lheisler commented 5 years ago

correction, there aren't currently pipeline scripts, these need to be added