need new Varscan tasks for somatic cancer CNV

chopdgd / bfx-tools-wdl

WDL tasks for commonly used BFX tools

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Closed mark-welsh closed 5 years ago

mark-welsh commented 5 years ago

This Varscan task only uses mpileup2cns but I need to use copynumber link and somatic link for CNV for somatic cancer.

I think its best to just make two new WDL tasks in the varscan/ directory

mark-welsh commented 5 years ago

@genomics-geek going to wait for your opinion on this before continuing

mark-welsh commented 5 years ago

just kidding I couldn't help myself ^^^