fix bug

inputs

@@ -1,6 +1,6 @@
 {
   "{{ project_name }}.bcftools_docker": "{{ bcftools_docker }}",
-  "{{ project_name }}.BCF": ["oss://share-data-temp/TNBC/vcf/FUSCCTNBC083_pon.vcf", "oss://share-data-temp/TNBC/vcf/FUSCCTNBC330_pon.vcf", "oss://share-data-temp/TNBC/vcf/FUSCCTNBC467_pon.vcf"],
+  "{{ project_name }}.vcf": {{ vcf }},
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}"
 }

tasks/bcftools.wdl

@@ -1,6 +1,6 @@
 task bcftools {
 
-	Array[File] bcfpon
+	Array[File] vcf
 	String docker
 	String cluster_config
 	String disk_size
@@ -10,7 +10,7 @@ task bcftools {
 		set -e
 		mkdir -p /cromwell_root/tmp/bcftools
 
-		for i in ${sep=" " bcfpon}
+		for i in ${sep=" " vcf}
 		do
 			bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$(basename $i.gz)
 			bcftools index /cromwell_root/tmp/bcftools/$(basename $i.gz) -f

tasks/bcftools1.wdl

@@ -1,31 +0,0 @@
-task bcftools {
-
-	File bcfpon
-	String docker
-	String cluster_config
-	String disk_size
-	Boolean PONmode
-
-
-	command <<<
-		set -o pipefail
-		set -e
-		
-		if [ ${PONmode} ]; then
-			bcftools view ${bcfpon} -Oz -o a.vcf.gz
-		else
-			echo 1
-		fi
-	>>>
-
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-	
-	output {
-		File vcf1="a.vcf.gz"
-	}
-}

workflow.wdl

@@ -5,11 +5,11 @@ workflow {{ project_name }} {
 	String bcftools_docker
 	String disk_size
 	String cluster_config
-	Array[File] BCF
+	Array[File] vcf
 
 	call bcftools.bcftools as bcftools {
 		input:
-		bcfpon=BCF,
+		vcf=vcf,
 		docker=bcftools_docker,
 		disk_size=disk_size,
 		cluster_config=cluster_config