Bug fix for Mitochondria Pipeline

[meganshand]

When I turned off NIO for the first task, I forgot to redo the disk size. This now includes the size of the input bam/cram as a part of the disk size.

[codecov-io]

Codecov Report

Merging #5861 into master will increase coverage by 6.885%.
The diff coverage is n/a.

@@              Coverage Diff               @@
##              master    #5861       +/-   ##
==============================================
+ Coverage     80.265%   87.15%   +6.885%     
- Complexity     30579    32899     +2320     
==============================================
  Files           1985     1985               
  Lines         147653   149287     +1634     
  Branches       16235    16607      +372     
==============================================
+ Hits          118513   130103    +11590     
+ Misses         23416    13216    -10200     
- Partials        5724     5968      +244

Impacted Files	Coverage Δ	Complexity Δ
...llbender/engine/spark/SparkCommandLineProgram.java	89.474% <0%> (-3.383%)	7% <0%> (+2%)
...tools/walkers/mutect/SomaticLikelihoodsEngine.java	91.045% <0%> (-1.978%)	31% <0%> (+13%)
...alkers/mutect/SomaticReferenceConfidenceModel.java	95.122% <0%> (-1.753%)	16% <0%> (+8%)
.../broadinstitute/hellbender/utils/QualityUtils.java	84.848% <0%> (-0.517%)	25% <0%> (+11%)
.../mutect/filtering/M2FiltersArgumentCollection.java	94.203% <0%> (-0.392%)	12% <0%> (+6%)
...ller/ReadThreadingAssemblerArgumentCollection.java	96.078% <0%> (-0.075%)	3% <0%> (+1%)
.../funcotator/filtrationRules/FuncotationFilter.java	100% <0%> (ø)	14% <0%> (+6%)	⬆️
...walkers/mutect/clustering/BetaBinomialCluster.java	100% <0%> (ø)	20% <0%> (+10%)	⬆️
...er/tools/walkers/mutect/Mutect2EngineUnitTest.java	100% <0%> (ø)	10% <0%> (+5%)	⬆️
...lbender/tools/walkers/mutect/clustering/Datum.java	100% <0%> (ø)	8% <0%> (+1%)	⬆️
... and 188 more