for loop

tasks/getBam.wdl

@@ -8,12 +8,9 @@ task getBam {
 	String disk_size
 	
 	command <<<
-		cat ${region} | whlie read a
-		do
+		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
-
+			/opt/conda/bin/samtools index $a.${sample}.bam; done
 	>>>
 
 	runtime {