split fastq and vcf

tasks/merge_family.wdl

@@ -15,6 +15,7 @@ task merge_family {
 	command <<<
 
 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfmerge --force-merge-all -o ${project}.family.vcf.gz ${D5_vcf} ${D6_vcf} ${F7_vcf} ${M8_vcf}
+		gunzip ${project}.family.vcf.gz 
 
 	>>>
 
@@ -25,7 +26,6 @@ task merge_family {
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File family_vcf = "${project}.family.vcf.gz"
-		File family_vcf_tbi = "${project}.family.vcf.gz.tbi"
+		File family_vcf = "${project}.family.vcf"
 	}
 }

workflow.wdl

@@ -735,7 +735,7 @@ workflow {{ project_name }} {
 			F7_vcf_tbi=benchmark_F7.rtg_vcf_index,
 			M8_vcf_tbi=benchmark_M8.rtg_vcf_index,
 			project=project,
-			docker=DIYdocker,
+			docker=BENCHMARKdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size,
 		}
@@ -868,7 +868,7 @@ workflow {{ project_name }} {
 			F7_vcf_tbi=benchmark_F7_vcf.rtg_vcf_index,
 			M8_vcf_tbi=benchmark_M8_vcf.rtg_vcf_index,
 			project=project,
-			docker=DIYdocker,
+			docker=BENCHMARKdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size,
 		}