Added a '--prefer-mane-transcripts' mode that enforces MANE_Select tagged Gencode transcripts where possible #4788

Job	Run time
check if the environment has privileges	1s
build and push gatk docker to artifacts	16m 30s
Validate generated WDLs using womtools	13m 59s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	25m 3s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	27m 58s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	24m 59s
Validate script WDLs using womtools	1m 1s
WDL test RUN_M2_WDL on cromwell	17m 27s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	13m 1s
Java 17.0.6+10 build and test cloud	18m 47s
Java 17.0.6+10 build and test integration	30m 17s
Java 17.0.6+10 build and test unit	18m 9s
Java 17.0.6+10 test on docker integration	35m 4s
Java 17.0.6+10 test on docker unit	20m 19s
Java 17.0.6+10 test on docker variantcalling	28m 16s
Java 17.0.6+10 test on docker conda	25m 22s
	5h 16m 13s

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