GGVCFs changes to revert "no data" calls to "./." and change GQ0 hom-refs to no-calls #3988

Job	Run time
build and push gatk docker to artifacts	25m 11s
check if the environment has privileges	1s
Validate generated WDLs using womtools	13m 36s
Validate script WDLs using womtools	1m 0s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	28m 31s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	30m 1s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	24m 41s
WDL test RUN_M2_WDL on cromwell	17m 56s
WDL test RUN_CNN_WDL on cromwell	17m 18s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	13m 11s
Java 17.0.6+10 build and test cloud	22m 44s
Java 17.0.6+10 build and test integration	34m 58s
Java 17.0.6+10 build and test unit	22m 44s
Java 17.0.6+10 test on docker integration	39m 14s
Java 17.0.6+10 test on docker unit	25m 26s
Java 17.0.6+10 test on docker variantcalling	28m 57s
Java 17.0.6+10 test on docker conda	33m 6s
	6h 18m 35s

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