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Adding funcotator stand-alone WDL to supported area #5999

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merged 3 commits into from
Jun 13, 2019

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jonn-smith
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Moves the funcotator.wdl to its own supported area with a README.

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codecov bot commented Jun 12, 2019

Codecov Report

Merging #5999 into master will decrease coverage by 35.111%.
The diff coverage is n/a.

@@               Coverage Diff                @@
##              master     #5999        +/-   ##
================================================
- Coverage     79.056%   43.945%   -35.111%     
+ Complexity     30765     20097     -10668     
================================================
  Files           2014      2014                
  Lines         151333    151333                
  Branches       16612     16612                
================================================
- Hits          119638     66503     -53135     
- Misses         25900     79634     +53734     
+ Partials        5795      5196       -599
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 1270 more

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Super minor comment. If you have tested this and it works, feel free to do the minor comment and merge.

# Handle our data sources:

# Extract the tar.gz:
echo "Extracting data sources zip file..."
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Not a zip file.

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Sure. But it is a GZip file...

Either way, fixed.

@jonn-smith jonn-smith merged commit 730164d into master Jun 13, 2019
@jonn-smith jonn-smith deleted the jts_funcotator_wdl_support branch June 13, 2019 16:37
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2 participants