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Build and Test GATK 4

Update dependencies to address security vulnerabilities, and add a se… #3509

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Update dependencies to address security vulnerabilities, and add a se…

Update dependencies to address security vulnerabilities, and add a se… #3509

Run time

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Job Run time
Validate script WDLs using womtools
1m 47s
Validate generated WDLs using womtools
16m 8s
build and push gatk docker to artifacts
23m 19s
check if the environment has privileges
1s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell
26m 18s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell
29m 57s
WDL test RUN_CNV_SOMATIC_WDL on cromwell
28m 39s
WDL test RUN_M2_WDL on cromwell
21m 34s
WDL test RUN_CNN_WDL on cromwell
19m 25s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell
16m 41s
Java 17.0.6+10 build and test cloud
16m 9s
Java 17.0.6+10 build and test integration
33m 8s
Java 17.0.6+10 build and test unit
23m 11s
Java 17.0.6+10 test on docker integration
39m 5s
Java 17.0.6+10 test on docker unit
27m 2s
Java 17.0.6+10 test on docker variantcalling
32m 7s
Java 17.0.6+10 test on docker conda
29m 41s
6h 24m 12s