修改输出路径

tasks/Dedup.wdl

@@ -1,9 +1,6 @@
 task Dedup {
-
-	String sample
-
 	File unsorted_bam
-
+	String sample
 	String docker
 	String cluster_config
 	String disk_size
@@ -12,13 +9,13 @@ 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 ${unsorted_bam} --output_dir ./
 	>>>
 	runtime {
 		docker:docker
-    	cluster: cluster_config
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    		cluster: cluster_config
+    		systemDisk: "cloud_ssd 40"
+    		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 
 	output {