Changed flow allele filtering in Mutect2 to work separately on the tumor and the normal samples #5992

Job	Run time
WDL test RUN_CNV_SOMATIC_WDL on cromwell	10m 58s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	25m 4s
Validate script WDLs using womtools	55s
WDL test RUN_M2_WDL on cromwell	19m 18s
build and push gatk docker to artifacts	12m 47s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	11m 37s
check if the environment has privileges	2s
Validate generated WDLs using womtools	14m 44s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	11m 53s
unit build and test Java 17.0.6+10	17m 44s
cloud build and test Java 17.0.6+10	3m 58s
integration build and test Java 17.0.6+10	30m 47s
conda test on docker Java 17.0.6+10	24m 37s
variantcalling test on docker Java 17.0.6+10	26m 45s
unit test on docker Java 17.0.6+10	19m 32s
integration test on docker Java 17.0.6+10	32m 13s
	4h 22m 54s

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