BQSR: avoid throwing an error when read group is missing in the recal table, and some refactoring. #4968

Job	Run time
build and push gatk docker to artifacts	11m 57s
Validate generated WDLs using womtools	14m 28s
check if the environment has privileges	1s
Validate script WDLs using womtools	3m 32s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	26m 27s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	26m 54s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	25m 9s
WDL test RUN_M2_WDL on cromwell	17m 23s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	12m 29s
Java 17.0.6+10 build and test cloud	18m 34s
Java 17.0.6+10 build and test integration	31m 19s
Java 17.0.6+10 build and test unit	17m 47s
Java 17.0.6+10 test on docker integration	35m 20s
Java 17.0.6+10 test on docker unit	19m 36s
Java 17.0.6+10 test on docker variantcalling	26m 29s
Java 17.0.6+10 test on docker conda	25m 24s
	5h 12m 49s

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