BQSR: avoid throwing an error when read group is missing in the recal table, and some refactoring. #4979

Job	Run time
check if the environment has privileges	3s
build and push gatk docker to artifacts	13m 44s
Validate generated WDLs using womtools	13m 55s
Validate script WDLs using womtools	1m 17s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	24m 38s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	26m 9s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	24m 14s
WDL test RUN_M2_WDL on cromwell	16m 51s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	12m 28s
Java 17.0.6+10 build and test cloud	17m 8s
Java 17.0.6+10 build and test integration	28m 16s
Java 17.0.6+10 build and test unit	17m 50s
Java 17.0.6+10 test on docker integration	33m 5s
Java 17.0.6+10 test on docker unit	20m 36s
Java 17.0.6+10 test on docker variantcalling	27m 28s
Java 17.0.6+10 test on docker conda	24m 2s
	5h 1m 44s

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