Add Mutect3 dataset generation to Mutect2 WDL

[davidbenjamin]

In addition, this PR removes Funcotator (these workflows don't need to be coupled),a bunch of code that juggles file names, and some obsolete and clunky means of handling defaults from the Mutect2 WDL. Also, it deletes the mutect2 multi-sample WDL which Terra renders unnecessary.

@takutosato Do you have time for one last code review?

[takutosato]

Yup looks good!

[davidbenjamin]

Thanks! I'll just fix the womtool failure on the pon WDL now.

[codecov]

Codecov Report

Merging #7992 (efd6394) into master (05a7634) will increase coverage by 7.358%.
The diff coverage is 50.000%.

@@               Coverage Diff               @@
##              master     #7992       +/-   ##
===============================================
+ Coverage     79.301%   86.659%   +7.358%     
- Complexity     36613     38769     +2156     
===============================================
  Files           2328      2328               
  Lines         181684    181685        +1     
  Branches       19950     19952        +2     
===============================================
+ Hits          144077    157447    +13370     
+ Misses         30805     17240    -13565     
- Partials        6802      6998      +196     

Impacted Files	Coverage Δ
...er/tools/walkers/annotator/AssemblyComplexity.java	97.333% <50.000%> (-1.315%)	⬇️
...tools/walkers/rnaseq/GeneExpressionEvaluation.java	89.286% <0.000%> (+0.397%)	⬆️
...llbender/tools/spark/sv/evidence/ReadMetadata.java	88.480% <0.000%> (+0.490%)	⬆️
.../walkers/vqsr/CNNScoreVariantsIntegrationTest.java	96.629% <0.000%> (+0.562%)	⬆️
...tmutpileup/ValidateBasicSomaticShortMutations.java	79.570% <0.000%> (+1.075%)	⬆️
...dinstitute/hellbender/tools/sv/SiteDepthtoBAF.java	82.418% <0.000%> (+1.099%)	⬆️
...lkers/validation/EvaluateInfoFieldConcordance.java	72.581% <0.000%> (+1.613%)	⬆️
...va/org/broadinstitute/hellbender/GATKBaseTest.java	98.333% <0.000%> (+1.667%)	⬆️
...kers/variantutils/UpdateVCFSequenceDictionary.java	86.207% <0.000%> (+1.724%)	⬆️
...ute/hellbender/tools/sv/CondenseDepthEvidence.java	80.488% <0.000%> (+2.439%)	⬆️
... and 208 more