VS-942. Fix an error where NO variants were found #2696

Job	Run time
build and push gatk docker to artifacts	18m 29s
Validate generated WDLs using womtools	14m 50s
Validate script WDLs using womtools	3m 45s
check if the environment has privileges	1s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	33m 3s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	46m 33s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	32m 26s
WDL test RUN_M2_WDL on cromwell	27m 26s
WDL test RUN_CNN_WDL on cromwell	27m 20s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	22m 53s
Java 8 build and test cloud	17m 51s
Java 11 build and test cloud	24m 24s
Java 11 build and test integration	42m 45s
Java 11 build and test unit	27m 23s
Java 8 test on docker integration	46m 54s
Java 8 test on docker unit	48m 13s
Java 8 test on docker variantcalling	46m 23s
Java 8 test on docker conda	32m 30s
	8h 33m 9s

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