GATK CNV MS Eval: Updated paths for internal bucket changes and updated GATK version

broadinstitute / gatk-evaluation

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Closed LeeTL1220 closed 5 years ago

LeeTL1220 commented 5 years ago

Updates the paths, which is necessary due to our internal bucket name changes.
Updated to 4.0.7.0
Removes implicit dependence on GATK jar override parameter. This required one task to be split into two tasks.
Making centromere track a parameter.

LeeTL1220 commented 5 years ago

@samuelklee This will also fix some issues @MartonKN is having.

samuelklee commented 5 years ago

@LeeTL1220 fine by me. I don't think we are requiring reviews in this repo just yet, so feel free to merge away!