BQSR: avoid throwing an error when read group is missing in the recal table, and some refactoring. #4969

Job	Run time
build and push gatk docker to artifacts	11m 53s
Validate generated WDLs using womtools	13m 31s
check if the environment has privileges	1s
Validate script WDLs using womtools	48s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	24m 23s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	27m 57s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	25m 21s
WDL test RUN_M2_WDL on cromwell	17m 34s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	12m 24s
Java 17.0.6+10 build and test cloud	15m 1s
Java 17.0.6+10 build and test integration	30m 55s
Java 17.0.6+10 build and test unit	18m 1s
Java 17.0.6+10 test on docker integration	34m 50s
Java 17.0.6+10 test on docker unit	20m 2s
Java 17.0.6+10 test on docker variantcalling	27m 9s
Java 17.0.6+10 test on docker conda	25m 20s
	5h 5m 10s

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