硬解码

tasks/Dedup.wdl

@@ -9,9 +9,9 @@ task Dedup {
 	command <<<
 		set -o pipefail
 		set -e
+		mv ${unsorted_bam} ./
 		/src/Bismark-0.18.2/deduplicate_bismark -p --bam ${unsorted_bam} 
-		outputdir= dirname ${unsorted_bam}
-		cp $outputdir${sample}_R1_bismark_bt2_pe.deduplicated.bam ./
+
 	>>>
 	runtime {
 		docker:docker