Fixed support for newer Gencode GTF versions #2687

Job	Run time
Validate script WDLs using womtools	1m 57s
build and push gatk docker to artifacts	29m 5s
Validate generated WDLs using womtools	13m 57s
check if the environment has privileges	1s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	33m 56s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	48m 31s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	36m 16s
WDL test RUN_M2_WDL on cromwell	27m 5s
WDL test RUN_CNN_WDL on cromwell	26m 10s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	28m 35s
Java 17.0.6+10 build and test cloud	21m 3s
Java 17.0.6+10 build and test integration	53m 30s
Java 17.0.6+10 build and test unit	34m 33s
Java 17.0.6+10 test on docker integration	47m 35s
Java 17.0.6+10 test on docker unit	29m 10s
Java 17.0.6+10 test on docker variantcalling	58m 19s
Java 17.0.6+10 test on docker conda	38m 16s
	8h 47m 59s

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