Migrate CleanVcf into GATK #733
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Description
This PR is intended to migrate the pipeline to leverage several new tools built in GATK to complete the CleanVcf workflow, as detailed in broadinstitute/gatk#8996. This is intended to introduce several enhancements over the existing implementation, including but not limited to:
Testing
Pre-Merge Changes Required
Remove automated syncing of WDL to Dockstore.