multiple file

inputs

@@ -1,10 +1,9 @@
 {
-  "{{project_name }}.bam_idx": "{{ bam_idx }}",
-  "{{project_name }}.region": "{{ region }}",
-  "{{project_name }}.disk_size": "100",
-  "{{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 }}.sample": "{{ sample }}"
-}
-
+  "{{ project_name }}.bam_idx": "{{ bam_idx }}",
+  "{{ project_name }}.disk_size": "100",
+  "{{ 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 }}.inputRegionsFile": "{{ inputRegionsFile }}",
+  "{{ project_name }}.sample": "{{ sample }}"
+}

workflow.wdl

@@ -2,22 +2,25 @@ import "./tasks/getBam.wdl" as getBam
 
 
 workflow {{ project_name }} {
+	File inputRegionsFile
+	Array[Array[File]] inputRegions = read_tsv(inputRegionsFile)
 	File bam
 	File bam_idx
 	String sample
-	String region
 	String docker
 	String cluster_config
 	String disk_size
 
-	call getBam.getBam as getBam {
-		input:	
-		bam=bam,
-		bam_idx=bam_idx,
-		sample=sample,
-		region=region,
-		docker=docker,
-		cluster_config=cluster_config,
-		disk_size=disk_size
+	scatter (Region in inputRegions) {
+		call getBam.getBam as getBam {
+			input:	
+			bam=bam,
+			bam_idx=bam_idx,
+			sample=sample,
+			region=Region[0],
+			docker=docker,
+			cluster_config=cluster_config,
+			disk_size=disk_size
+		}
 	}
 }