Migrate CleanVcf into GATK

[kjaisingh]

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:

• Introduce various unit and integration tests into the workflow.
• Create more robust and generalizable tools that can be used independent of CleanVcf.
• Improve runtime and execution speed by leveraging Java.

Testing

• This Terra job shows an example run of the pipeline prior to this change.
• This Terra job shows an example run of the pipeline with this change. You can compare the output VCF files to see the lack of difference between the two.
• Validated all WDLs with womtool.

Pre-Merge Changes Required

Remove automated Dockstore image sync for development branch.