merged_gvcf

tasks/GVCFtyper.wdl

@@ -26,8 +26,8 @@ command <<<
 	}
 
 	output {
-		File gvcf = "${project}.joint.g.vcf"
-		File gvcf_idx = "${project}.joint.g.vcf.idx"
+		File merged_gvcf = "${project}.joint.g.vcf"
+		File merged_gvcf_idx = "${project}.joint.g.vcf.idx"
 	}
 }
 

tasks/split_gvcf_files.wdl

@@ -1,5 +1,5 @@
  task split_gvcf_files {
-	File gvcf
+	File merged_gvcf
 	String project
 	String docker
 	String cluster_config
@@ -7,14 +7,14 @@
 	
 	command <<<
 
-		cat ${gvcf} | grep '#CHROM' | sed s'/\t/\n/g' > name
+		cat ${merged_gvcf} | grep '#CHROM' | sed s'/\t/\n/g' > name
 
 		ncol=`cat name | wc -l`
 
 		sed -i '1,9d' name
 
-		cat ${gvcf} | grep '#' > header
-		cat ${gvcf} | grep -v '#' > body
+		cat ${merged_gvcf} | grep '#' > header
+		cat ${merged_gvcf} | grep -v '#' > body
 		cat body | grep -w '^chr1\|^chr2\|^chr3\|^chr4\|^chr5\|^chr6\|^chr7\|^chr8\|^chr9\|^chr10\|^chr11\|^chr12\|^chr13\|^chr14\|^chr15\|^chr16\|^chr17\|^chr18\|^chr19\|^chr20\|^chr21\|^chr22\|^chrX' > body.filtered
 		cat header body.filtered > ${project}.filtered.g.vcf
 

workflow.wdl

@@ -46,7 +46,7 @@ workflow {{ project_name }} {
 
 	call split_gvcf_files.split_gvcf_files as split_gvcf_files {
 		input:
-		gvcf=gvcf,
+		merged_gvcf=GVCFtyper.merged_gvcf,
 		docker=DIYdocker,
 		project=project,
 		cluster_config=SMALLcluster_config,