gunzip

tasks/benchmark.wdl

 
 		export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa
 
-		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip ${vcf} -c > ${sample}.rtg.vcf.gz
+
+		gunzip ${vcf} -c > unzip.vcf
+ 
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip unzip.vcf -c > ${sample}.rtg.vcf.gz
 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.rtg.vcf.gz
 
 		if [[ ${sample} =~ "LCL5" ]];then

tasks/merge_mendelian.wdl

-task merge_mendelian {
+ctask merge_mendelian {
 	File D5_trio_vcf
 	File D6_trio_vcf
 	File family_vcf