新思路

tasks/Dedup.wdl

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