Updating Picard version in mitochondria WDL

[meganshand]

This update means the pipeline won't die on single-ended reads (it just filters them out).

[codecov-io]

Codecov Report

Merging #5818 into master will decrease coverage by 67.99%.
The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #5818       +/-   ##
===============================================
- Coverage     87.031%   19.041%   -67.99%     
+ Complexity     32107      4583    -27524     
===============================================
  Files           1972      1234      -738     
  Lines         147194     71206    -75988     
  Branches       16201     11401     -4800     
===============================================
- Hits          128104     13558   -114546     
- Misses         13184     55608    +42424     
+ Partials        5906      2040     -3866

Impacted Files	Coverage Δ	Complexity Δ
...hellbender/engine/spark/IntervalWalkerContext.java	0% <0%> (-100%)	0% <0%> (-5%)
...ls/walkers/mutect/filtering/BaseQualityFilter.java	0% <0%> (-100%)	0% <0%> (-6%)
...nder/tools/readersplitters/SampleNameSplitter.java	0% <0%> (-100%)	0% <0%> (-2%)
...broadinstitute/hellbender/utils/svd/SimpleSVD.java	0% <0%> (-100%)	0% <0%> (-5%)
...lbender/tools/walkers/mutect/clustering/Datum.java	0% <0%> (-100%)	0% <0%> (-7%)
...ark/AssemblyRegionReadShardArgumentCollection.java	0% <0%> (-100%)	0% <0%> (-1%)
.../examples/metrics/single/ExampleSingleMetrics.java	0% <0%> (-100%)	0% <0%> (-4%)
...groups/StructuralVariantDiscoveryProgramGroup.java	0% <0%> (-100%)	0% <0%> (-3%)
...ls/variant/writers/GVCFBlockCombiningIterator.java	0% <0%> (-100%)	0% <0%> (-1%)
.../tools/copynumber/utils/MergeAnnotatedRegions.java	0% <0%> (-100%)	0% <0%> (-3%)
... and 1800 more

[ldgauthier]

Without seeing the dockerfile I don't actually know what changed. Is that a Picard jar from master in there or just a branch?

[meganshand]

Good point, here's the PR in dsde-pipelines: https://github.com/broadinstitute/dsde-pipelines/pull/718/files

It just updates the Picard version.

[ldgauthier]

Looks good!

Can you note the single-end fix in the commit message so it magically propagates to the release notes?

Meanwhile I'm going to go cry over the fact that GATK4beta5 is still in the GitC docker.

[jsotobroad]

great PR!