first commit

tasks/index.wdl

@@ -8,7 +8,7 @@ task index {
 	
 	command <<<
 		mv ${snv_gzvcf} ./${sample}.snv.vcf.gz
-		mv ${indel_gzvcf} ./${sample.indel.vcf.gz}
+		mv ${indel_gzvcf} ./${sample}.indel.vcf.gz
 		rtg index -f vcf ${sample}.snv.vcf.gz
 		rtg index -f vcf ${sample}.indel.vcf.gz
 	>>>
@@ -20,6 +20,8 @@ task index {
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
+		File snv_gzvcf_2 = "${sample}.snv.vcf.gz"
+		File indel_gzvcf_2 = "${sample}.indel.vcf.gz"
 		File snv_gzvcf_index = "${sample}.snv.vcf.gz.tbi"
 		File indel_gzvcf_index = "${sample}.indel.vcf.gz.tbi"
 	}

tasks/merge.wdl

@@ -1,6 +1,6 @@
 task merge {
-	File snv_gzvcf
-	File indel_gzvcf
+	File snv_gzvcf_2
+	File indel_gzvcf_2
 	File snv_gzvcf_index
 	File indel_gzvcf_index
 	String sample
@@ -9,7 +9,7 @@ task merge {
 	String disk_size
 	
 	command <<<
-		bcftools concat -a ${snv_gzvcf} ${indel_gzvcf} > ${sample}.vcf
+		bcftools concat -a ${snv_gzvcf_2} ${indel_gzvcf_2} > ${sample}.vcf
 	>>>
 
 	runtime {

workflow.wdl

@@ -19,6 +19,8 @@ workflow {{ project_name }} {
 
 	call merge.merge as merge {
 		input:
+		snv_gzvcf_2=index.snv_gzvcf_2,
+		indel_gzvcf_2=index.indel_gzvcf_2,
 		snv_gzvcf=snv_gzvcf,
 		indel_gzvcf=indel_gzvcf,
 		snv_gzvcf_index=index.snv_gzvcf_index,