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Update cromwell and womtool from v51 to v59.
Update cromwell and womtool. See if I feel lucky.
Codecov Report
Merging #7824 (d5011db) into master (72684d0) will increase coverage by
0.006%
. The diff coverage isn/a
.
:exclamation: Current head d5011db differs from pull request most recent head ed1faba. Consider uploading reports for the commit ed1faba to get more accurate results
@@ Coverage Diff @@
## master #7824 +/- ##
===============================================
+ Coverage 86.948% 86.954% +0.006%
+ Complexity 36927 36897 -30
===============================================
Files 2219 2214 -5
Lines 173673 173540 -133
Branches 18755 18736 -19
===============================================
- Hits 151006 150900 -106
+ Misses 16055 16039 -16
+ Partials 6612 6601 -11
Impacted Files | Coverage Δ | |
---|---|---|
.../hellbender/utils/python/PythonUnitTestRunner.java | 75.410% <0.000%> (-3.279%) |
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...roadinstitute/hellbender/utils/read/ReadUtils.java | 81.646% <0.000%> (-0.633%) |
:arrow_down: |
...tute/hellbender/engine/AssemblyRegionIterator.java | 92.632% <0.000%> (-0.152%) |
:arrow_down: |
...ples/ExampleMultiFeatureWalkerIntegrationTest.java | 91.566% <0.000%> (-0.100%) |
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...broadinstitute/hellbender/utils/read/GATKRead.java | 57.377% <0.000%> (ø) |
|
...titute/hellbender/tools/walkers/sv/SVAnnotate.java | 98.701% <0.000%> (ø) |
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.../hellbender/tools/walkers/GenotypeGVCFsEngine.java | 90.826% <0.000%> (ø) |
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...notyper/GenotypeCalculationArgumentCollection.java | 89.474% <0.000%> (ø) |
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...otypecaller/HaplotypeCallerArgumentCollection.java | 100.000% <0.000%> (ø) |
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...typecaller/LikelihoodEngineArgumentCollection.java | 100.000% <0.000%> (ø) |
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... and 9 more |
Cromwell switched to Java 11 starting with version 60 so the Java 8 sub-builds are probably going to error like
Caused by: java.lang.UnsupportedClassVersionError: wdl/draft3/parser/WdlParser$Ast has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:756)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:473)
@mcovarr Ouch. Well, thanks for the update - I guess we'll add that to the long list of reasons to move off of Java 8.
Closing in favor of https://github.com/broadinstitute/gatk/pull/8035.