VS-1476. Removing All usage of VQSR from VDS creation. #4794

Job	Run time
build and push gatk docker to artifacts	42m 45s
Validate generated WDLs using womtools	13m 13s
Validate script WDLs using womtools	51s
check if the environment has privileges	1s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	1h 0m 32s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	1h 2m 25s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	58m 0s
WDL test RUN_M2_WDL on cromwell	9m 46s
WDL test RUN_CNN_WDL on cromwell	42m 38s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	40m 38s
Java 17.0.6+10 build and test cloud	16m 53s
Java 17.0.6+10 build and test integration	33m 36s
Java 17.0.6+10 build and test unit	21m 26s
Java 17.0.6+10 test on docker integration	40m 12s
Java 17.0.6+10 test on docker unit	24m 38s
Java 17.0.6+10 test on docker variantcalling	32m 51s
Java 17.0.6+10 test on docker conda	30m 39s
	8h 51m 4s

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