...

tasks/Dedup.wdl

@@ -9,7 +9,9 @@ task Dedup {
 	command <<<
 		set -o pipefail
 		set -e
-		/src/Bismark-0.18.2/deduplicate_bismark -p --bam ${unsorted_bam} --output_dir ./
+		/src/Bismark-0.18.2/deduplicate_bismark -p --bam ${unsorted_bam} 
+		outputdir= dirname ${unsorted_bam}
+		cp ${outputdir} ./
 	>>>
 	runtime {
 		docker:docker