multiple pos at the same time

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 }}.region": "{{ region }}",
+  "{{ project_name }}.pos": "{{ pos_list.split(";") | tojson }}",
   "{{ project_name }}.sample": "{{ sample }}"
-}
+}

tasks/getBam.wdl

@@ -2,17 +2,14 @@ task getBam {
 	File bam
 	File bam_idx
 	String sample
-	File region
+	File pos
 	String docker
 	String cluster_config
 	String disk_size
 	
 	command <<<
-		cat ${region} | while read a
-		do
-			/opt/conda/bin/samtools view -b ${bam} "$a" > $a.${sample}.bam
-			/opt/conda/bin/samtools index $a.${sample}.bam
-		done
+			/opt/conda/bin/samtools view ${bam} -H ${sep=" " pos} | /opt/conda/bin/samtools view -bS - | /opt/conda/bin/samtools sort > ${sample}.bam
+			/opt/conda/bin/samtools index ${sample}.bam
 	>>>
 
 	runtime {
@@ -22,7 +19,8 @@ task getBam {
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		Array[File] region_bam = glob("*.bam")
-		Array[File] region_bai = glob("*.bam.bai")
+		File sub_bam = "${sample}.bam"
+		File sub_bai = "${sample}.bam.bai"
 	}
 }
+

workflow.wdl

@@ -2,9 +2,10 @@ import "./tasks/getBam.wdl" as getBam
 
 
 workflow {{ project_name }} {
-	File region
+	
 	File bam
 	File bam_idx
+	Array[String] pos
 	String sample
 	String docker
 	String cluster_config
@@ -15,7 +16,7 @@ workflow {{ project_name }} {
 		bam=bam,
 		bam_idx=bam_idx,
 		sample=sample,
-		region=region,
+		pos=pos,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size