VS-1466 restructure export vcf for copy reasons #4608

Job	Run time
check if the environment has privileges	1s
Validate generated WDLs using womtools	13m 1s
build and push gatk docker to artifacts	26m 59s
Validate script WDLs using womtools	1m 5s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	29m 25s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	33m 24s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	31m 58s
WDL test RUN_M2_WDL on cromwell	23m 53s
WDL test RUN_CNN_WDL on cromwell	22m 1s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	18m 52s
Java 17.0.6+10 build and test cloud	18m 49s
Java 17.0.6+10 build and test integration	32m 52s
Java 17.0.6+10 build and test unit	19m 54s
Java 17.0.6+10 test on docker integration	38m 2s
Java 17.0.6+10 test on docker unit	22m 45s
Java 17.0.6+10 test on docker variantcalling	33m 21s
Java 17.0.6+10 test on docker conda	30m 15s
	6h 36m 37s

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