Enable passing a threshold to govern the window for detection of dispersed deletions

[kjaisingh]

Description

This PR is intended to enable passing in a custom breakpoint cutoff for dispersed duplication detection for complex events in GATK-SV. It also sets this cutoff as 5000 by default, as opposed to 1000000 in the existing implementation.

Testing

• The following job represents a run of the original WDL.
• The following job represents a run of the modified WDL with the original value of 1000000 passed - the number of variants in the output VCF is equal to the original case.
• The following job represents a run of the modified WDL with the default value of 5000 passed - the number of variants in the output VCF is still equal to the original case, but 3 out of the 5 variants in the Chromosome 1 VCF with a CPX_TYPE of dupINV are revised to dDUP.
• Validated all WDLs with womtool.

Pre-Merge Changes Required

Remove automated sync of the GenotypeComplexVariants WDL to Dockstore.

[kjaisingh]

@mwalker174 One thing to note here - default for this is currently 1000000 to match what's currently in GATK-SV, let me know if you think I should reduce this though.

[mwalker174]

Thanks this looks ok, and let's set the threshold to 5000 as discussed offline

[kjaisingh]

Retested with updated default, merging now.

[VJalili]

@kjaisingh please undo this in another PR; no need to have a PR only for this, it can go as part of an existing PR.

[kjaisingh]

Hi Vahid, thanks for pointing this out - yes, I made #866 in light of this, but will include it in another PR if I merge one soon. Apologies for the inconvenience.

[VJalili]

Thanks! I would remove it as part of one of your relevant PRs.