.

tasks/Dedup.wdl

@@ -12,7 +12,7 @@ task Dedup {
 		/src/Bismark-0.18.2/deduplicate_bismark -p --bam ${unsorted_bam} 
 		outputdir= dirname ${unsorted_bam}
 		bam= "${sample}_R1_bismark_bt2_pe.deduplicated.bam"
-		cp ${outputdir}/${bam} ./
+		cp $outputdir/$bam ./
 	>>>
 	runtime {
 		docker:docker