新思路

tasks/Dedup.wdl

@@ -10,8 +10,8 @@ task Dedup {
 		set -o pipefail
 		set -e
 		mv ${unsorted_bam} ./
-		/src/Bismark-0.18.2/deduplicate_bismark -p --bam ${unsorted_bam} 
-
+		input = basename ${unsorted_bam}
+		/src/Bismark-0.18.2/deduplicate_bismark -p --bam ./$input 
 	>>>
 	runtime {
 		docker:docker