single input

inputs

@@ -4,6 +4,6 @@
   "{{ project_name }}.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
   "{{ project_name }}.bam": "{{ bam }}",
-  "{{ project_name }}.pos": {{ pos_list | tojson }},
+  "{{ project_name }}.pos": {{ pos }},
   "{{ project_name }}.sample": "{{ sample }}"
 }

tasks/getBam.wdl

@@ -2,14 +2,14 @@ task getBam {
 	File bam
 	File bam_idx
 	String sample
-	Array[String] pos
+	String pos
 	String docker
 	String cluster_config
 	String disk_size
 	
 	command <<<
-			/opt/conda/bin/samtools view -b ${bam} ${sep=" " pos} | /opt/conda/bin/samtools sort - > ${sample}.bam
-			/opt/conda/bin/samtools index ${sample}.bam
+			/opt/conda/bin/samtools view -b ${bam} ${pos} > ${sample}.${pos}.bam
+			/opt/conda/bin/samtools index ${sample}.${pos}.bam
 	>>>
 
 	runtime {
@@ -19,8 +19,8 @@ task getBam {
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File sub_bam = "${sample}.bam"
-		File sub_bai = "${sample}.bam.bai"
+		File sub_bam = "${sample}.${pos}.bam"
+		File sub_bai = "${sample}.${pos}.bam.bai"
 	}
 }
 

workflow.wdl

@@ -5,7 +5,7 @@ workflow {{ project_name }} {
 	
 	File bam
 	File bam_idx
-	Array[String] pos
+	String pos
 	String sample
 	String docker
 	String cluster_config