Add haploid support to GnarlyGenotyper #2774

Job	Run time
Validate script WDLs using womtools	2m 18s
build and push gatk docker to artifacts	31m 19s
check if the environment has privileges	1s
Validate generated WDLs using womtools	15m 55s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	42m 21s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	52m 9s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	36m 3s
WDL test RUN_M2_WDL on cromwell	27m 40s
WDL test RUN_CNN_WDL on cromwell	24m 54s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	23m 46s
Java 17.0.6+10 build and test cloud	17m 50s
Java 17.0.6+10 build and test integration	42m 13s
Java 17.0.6+10 build and test unit	26m 53s
Java 17.0.6+10 test on docker integration	1h 0m 53s
Java 17.0.6+10 test on docker unit	30m 36s
Java 17.0.6+10 test on docker variantcalling	56m 5s
Java 17.0.6+10 test on docker conda	49m 29s
	9h 0m 25s

Provide feedback