Upgrade to gradle 5.4.1

[tomwhite]

We are two major versions behind the latest gradle release. A later version is needed for upgrading Spark (#5990) and using BigQuery (#5928).

[codecov]

Codecov Report

Merging #6007 into master will decrease coverage by 51.742%.
The diff coverage is n/a.

@@               Coverage Diff                @@
##              master     #6007        +/-   ##
================================================
- Coverage     86.931%   35.189%   -51.742%     
+ Complexity     32754     17310     -15444     
================================================
  Files           2016      2011         -5     
  Lines         151426    150912       -514     
  Branches       16623     16131       -492     
================================================
- Hits          131636     53105     -78531     
- Misses         13728     92939     +79211     
+ Partials        6062      4868      -1194

Impacted Files	Coverage Δ	Complexity Δ
...ls/variant/writers/GVCFBlockCombiningIterator.java	0% <0%> (-100%)	0% <0%> (-1%)
...ls/walkers/genotyper/HeterogeneousPloidyModel.java	0% <0%> (-100%)	0% <0%> (-14%)
...nder/utils/downsampling/FractionalDownsampler.java	0% <0%> (-100%)	0% <0%> (-17%)
...park/pathseq/MarkedOpticalDuplicateReadFilter.java	0% <0%> (-100%)	0% <0%> (-4%)
...otypecaller/RandomLikelihoodCalculationEngine.java	0% <0%> (-100%)	0% <0%> (-6%)
...r/utils/solver/UnivariateSolverSpecifications.java	0% <0%> (-100%)	0% <0%> (-4%)
...ute/hellbender/utils/hmm/UninformativeTestHMM.java	0% <0%> (-100%)	0% <0%> (-5%)
...ender/utils/svd/OjAlgoSingularValueDecomposer.java	0% <0%> (-100%)	0% <0%> (-3%)
...typer/afcalc/OriginalDiploidExactAFCalculator.java	0% <0%> (-100%)	0% <0%> (-15%)
...groups/StructuralVariantDiscoveryProgramGroup.java	0% <0%> (-100%)	0% <0%> (-3%)
... and 1384 more

[tomwhite]

@lbergelson are you able to help with the docker/gradle failures? Also, there are likely more gradle changes needed for publishing artifacts, but I'm not sure what's needed or how to test those changes.

[droazen]

@tomwhite You need to update dockertest.gradle as well. The needed change is in my PR here: https://github.com/broadinstitute/gatk/pull/5928/files#diff-20d46fff5956131a01d67961f7ec15c0

[tomwhite]

Thanks @droazen, that fixes it. All the tests now pass. Are there any other changes needed before merging?

[droazen]

@lbergelson suggested that we test the maven artifact uploading, as he suspects it might break in this PR. We'll test that soon and get back to you on the results.

[lbergelson]

I fixed a deprecation warning and rebuild the wrapper itself. Haven't changed the publishing over yet.

[lbergelson]

I fixed the artifact uploading as well now. Everything should be good provided tests are passing. It turned out to be something really simple and dumb.