Fixed support for newer Gencode GTF versions by making the GencodeGTF… #2698

Job	Run time
build and push gatk docker to artifacts	27m 15s
Validate script WDLs using womtools	3m 5s
check if the environment has privileges	2s
Validate generated WDLs using womtools	14m 24s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	35m 4s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	51m 49s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	35m 52s
WDL test RUN_M2_WDL on cromwell	27m 21s
WDL test RUN_CNN_WDL on cromwell	29m 17s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	24m 47s
Java 17.0.6+10 build and test cloud	20m 52s
Java 17.0.6+10 build and test integration	43m 32s
Java 17.0.6+10 build and test unit	34m 8s
Java 17.0.6+10 test on docker integration	47m 2s
Java 17.0.6+10 test on docker unit	29m 40s
Java 17.0.6+10 test on docker variantcalling	59m 28s
Java 17.0.6+10 test on docker conda	47m 6s
	8h 50m 44s

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