Allow custom ploidy regions in HaplotypeCaller #3485

Job	Run time
Validate script WDLs using womtools	1m 21s
Validate generated WDLs using womtools	13m 5s
build and push gatk docker to artifacts	25m 20s
check if the environment has privileges	1s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	26m 28s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	27m 50s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	28m 44s
WDL test RUN_M2_WDL on cromwell	20m 11s
WDL test RUN_CNN_WDL on cromwell	20m 57s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	16m 27s
Java 17.0.6+10 build and test cloud	15m 9s
Java 17.0.6+10 build and test integration	33m 32s
Java 17.0.6+10 build and test unit	19m 33s
Java 17.0.6+10 test on docker integration	37m 11s
Java 17.0.6+10 test on docker unit	24m 55s
Java 17.0.6+10 test on docker variantcalling	32m 0s
Java 17.0.6+10 test on docker conda	31m 14s
	6h 13m 58s

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