Gave SortSam lenient validation in M2 wdl

[davidbenjamin]

@takutosato this fixes a bug that came up this morning when I was trying to make a bamout for one of Junko's samples.

[codecov-io]

Codecov Report

Merging #4844 into master will increase coverage by 0.21%.
The diff coverage is n/a.

@@             Coverage Diff              @@
##             master    #4844      +/-   ##
============================================
+ Coverage     80.37%   80.58%   +0.21%     
- Complexity    17677    18143     +466     
============================================
  Files          1088     1088              
  Lines         64006    65206    +1200     
  Branches      10312    10622     +310     
============================================
+ Hits          51444    52548    +1104     
- Misses         8554     8603      +49     
- Partials       4008     4055      +47

Impacted Files	Coverage Δ	Complexity Δ
...der/tools/walkers/mutect/M2ArgumentCollection.java	93.54% <0%> (-0.9%)	6% <0%> (+3%)
...ools/walkers/annotator/VariantAnnotatorEngine.java	92.23% <0%> (-0.86%)	123% <0%> (+49%)
...itute/hellbender/tools/walkers/mutect/Mutect2.java	90.9% <0%> (-0.76%)	27% <0%> (+12%)
...org/broadinstitute/hellbender/engine/GATKTool.java	91.38% <0%> (-0.13%)	163% <0%> (+69%)
...institute/hellbender/engine/VariantWalkerBase.java	100% <0%> (ø)	21% <0%> (+10%)	⬆️
...otypecaller/HaplotypeCallerArgumentCollection.java	100% <0%> (ø)	4% <0%> (+2%)	⬆️
...efaultGATKVariantAnnotationArgumentCollection.java	100% <0%> (ø)	11% <0%> (+6%)	⬆️
...titute/hellbender/tools/walkers/GenotypeGVCFs.java	90.55% <0%> (+0.46%)	50% <0%> (+3%)	⬆️
...nder/tools/spark/pipelines/ReadsPipelineSpark.java	90.47% <0%> (+0.68%)	25% <0%> (+11%)	⬆️
...stitute/hellbender/tools/HaplotypeCallerSpark.java	84.17% <0%> (+1.01%)	40% <0%> (+15%)	⬆️
... and 10 more

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