更改

tasks/Dedup.wdl

@@ -10,8 +10,8 @@ task Dedup {
 		set -o pipefail
 		set -e
 		cp ${unsorted_bam} ./
-		input = basename ${unsorted_bam}
-		/src/Bismark-0.18.2/deduplicate_bismark -p --bam ./${input}
+		inputfile = basename ${unsorted_bam}
+		/src/Bismark-0.18.2/deduplicate_bismark -p --bam ./$inputfile
 	>>>
 	runtime {
 		docker:docker
@@ -21,7 +21,8 @@ task Dedup {
 	}
 
 	output {
-		File Dedup_bam = "${sample}_R1_bismark_bt2_pe.deduplicated.bam"
+		File dedup_bam = "${sample}_R1_bismark_bt2_pe.deduplicated.bam"
+		File dedup_repoet = "${sample}_R1_bismark_bt2_pe.deduplication_report.txt"
 	}
 }