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Update cromwell and womtool from v51 to v59.

Open cmnbroad opened this issue 2 years ago • 3 comments

Update cromwell and womtool. See if I feel lucky.

cmnbroad avatar May 02 '22 19:05 cmnbroad

Codecov Report

Merging #7824 (d5011db) into master (72684d0) will increase coverage by 0.006%. The diff coverage is n/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%) :arrow_down:
...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%) :arrow_down:
...broadinstitute/hellbender/utils/read/GATKRead.java 57.377% <0.000%> (ø)
...titute/hellbender/tools/walkers/sv/SVAnnotate.java 98.701% <0.000%> (ø)
.../hellbender/tools/walkers/GenotypeGVCFsEngine.java 90.826% <0.000%> (ø)
...notyper/GenotypeCalculationArgumentCollection.java 89.474% <0.000%> (ø)
...otypecaller/HaplotypeCallerArgumentCollection.java 100.000% <0.000%> (ø)
...typecaller/LikelihoodEngineArgumentCollection.java 100.000% <0.000%> (ø)
... and 9 more

codecov[bot] avatar May 02 '22 20:05 codecov[bot]

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 avatar May 03 '22 13:05 mcovarr

@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.

cmnbroad avatar May 03 '22 13:05 cmnbroad

Closing in favor of https://github.com/broadinstitute/gatk/pull/8035.

cmnbroad avatar Sep 26 '22 14:09 cmnbroad