VS-1476. Removing All usage of VQSR from VDS creation. #4787

Job	Run time
build and push gatk docker to artifacts	38m 41s
Validate script WDLs using womtools	52s
check if the environment has privileges	1s
Validate generated WDLs using womtools	13m 13s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	57m 1s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	1h 0m 32s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	54m 37s
WDL test RUN_M2_WDL on cromwell	45m 53s
WDL test RUN_CNN_WDL on cromwell	55m 45s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	40m 30s
Java 17.0.6+10 build and test cloud	16m 17s
Java 17.0.6+10 build and test integration	30m 59s
Java 17.0.6+10 build and test unit	20m 56s
Java 17.0.6+10 test on docker integration	38m 17s
Java 17.0.6+10 test on docker unit	25m 13s
Java 17.0.6+10 test on docker variantcalling	34m 26s
Java 17.0.6+10 test on docker conda	30m 26s
	9h 23m 39s

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