for loop

tasks/getBam.wdl

@@ -8,8 +8,11 @@ task getBam {
 	String disk_size
 	
 	command <<<
-		/opt/conda/bin/samtools view -b ${bam} "${region}" > ${region}.${sample}.bam
-		/opt/conda/bin/samtools index ${region}.${sample}.bam
+		cat ${region} | whlie read a
+		do
+			/opt/conda/bin/samtools view -b ${bam} "$a" > $a.${sample}.bam
+			/opt/conda/bin/samtools index $a.${sample}.bam
+		done
 
 	>>>
 
@@ -20,7 +23,7 @@ task getBam {
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File region_bam = "${region}.${sample}.bam"
-		File region_bai = "${region}.${sample}.bam.bai"
+		Array[File] region_bam = glob("*.bam")
+		Array[File] region_bai = glob("*.bam.bai")
 	}
 }

workflow.wdl

@@ -3,7 +3,6 @@ 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
@@ -11,16 +10,15 @@ workflow {{ project_name }} {
 	String cluster_config
 	String 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
-		}
+	call getBam.getBam as getBam {
+		input:	
+		bam=bam,
+		bam_idx=bam_idx,
+		sample=sample,
+		region=inputRegionsFile,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
 	}
 }
+