BQSR: restore ability to specify custom covariates and to disable standard covariates. (Take 2) #5663

Job	Run time
Validate script WDLs using womtools	1m 7s
build and push gatk docker to artifacts	12m 37s
Validate generated WDLs using womtools	14m 14s
check if the environment has privileges	2s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	26m 13s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	25m 8s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	25m 6s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	13m 6s
WDL test RUN_M2_WDL on cromwell	18m 10s
unit build and test Java 17.0.6+10	18m 31s
cloud build and test Java 17.0.6+10	16m 5s
integration build and test Java 17.0.6+10	29m 35s
conda test on docker Java 17.0.6+10	24m 51s
unit test on docker Java 17.0.6+10	37m 25s
variantcalling test on docker Java 17.0.6+10	25m 25s
integration test on docker Java 17.0.6+10	32m 20s
	5h 19m 55s

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