Merge pull request #41 from nakib103/gencode_primary

Enable gencode primary in VEP config

Author: likhitha-surapaneni

nextflow/vcf_prepper/bin/generate_vep_config.py

@@ -635,6 +635,7 @@ def main(args=None):
         file.write("variant_class 1\n")
         file.write("protein 1\n")
         file.write("transcript_version 1\n")
+        file.write("gencode_primary 1\n")
 
         if args.cache_dir:
             file.write(f"cache_version {version}\n")