VS-942. Fix an error where NO variants were found #2694

Job	Run time
build and push gatk docker to artifacts	24m 9s
Validate generated WDLs using womtools	15m 35s
Validate script WDLs using womtools	3m 18s
check if the environment has privileges	2s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	39m 7s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	51m 17s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	32m 27s
WDL test RUN_M2_WDL on cromwell	27m 16s
WDL test RUN_CNN_WDL on cromwell	27m 3s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	22m 24s
Java 8 build and test cloud	25m 0s
Java 11 build and test cloud	29m 25s
Java 11 build and test integration	43m 1s
Java 11 build and test unit	30m 29s
Java 8 test on docker integration	50m 36s
Java 8 test on docker unit	50m 38s
Java 8 test on docker variantcalling	39m 57s
Java 8 test on docker conda	40m 58s
	9h 12m 42s

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