Alter: MD5.wdl

README.md

@@ -28,6 +28,11 @@ choppy batch YaqingLiu/MD5-latest samples.json -p project_name
 ```Json
 {
     "sample_id": "sample_id",
-    "files": ["A", "B", "C", ..., "Z"]
+    "INPUT": [
+		"file_1",
+		"file_2",
+		"file_3",
+		...,
+		"file_n"]
 }
 ```

tasks/MD5.wdl

@@ -6,10 +6,14 @@ task MD5 {
 	String disk_size
 
 	command <<<
-		for file in ${sep=" " INPUT}
+		set -o pipefail
+		set -e
+
+		for i in ${sep=" " INPUT}
 		do
-			md5sum ${file} > ${file}.md5
+			md5sum $i > $i.md5
 		done
+
 		cat `ls | grep .md5$` > OUTPUT.md5
 	>>>