.....

tasks/Dedup.wdl

@@ -11,7 +11,8 @@ task Dedup {
 		set -e
 		/src/Bismark-0.18.2/deduplicate_bismark -p --bam ${unsorted_bam} 
 		outputdir= dirname ${unsorted_bam}
-		cd $outputdir
+		bam= ${sample}_R1_bismark_bt2_pe.deduplicated.bam
+		cp $outputdir/$bam ./
 	>>>
 	runtime {
 		docker:docker