Alter: batch calculation

README.md

@@ -0,0 +1,33 @@
+# README.md
+
+> Author: Yaqing Liu
+>
+> Email: [yaqing.liu@outlook.com](mailto:yaqing.liu@outlook.com)
+> 
+> Last Updates: 08/04/2021
+
+This app will generate the MD5 
+#### Requirements
+
+- choppy
+- Ali-Cloud
+- Linux
+
+#### Usage
+```Shell
+# Install
+choppy install YaqingLiu/MD5
+
+# Prepare the input file: samples.json
+
+# Submit your task
+choppy batch YaqingLiu/MD5-latest samples.json -p project_name
+```
+
+#### Input
+```Json
+{
+    "sample_id": "sample_id",
+    "files": ["A", "B", "C", ..., "Z"]
+}
+```

defaults

@@ -1,5 +1,5 @@
 {
     "docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/r-base:4.0.2",
-    "disk_size": "200",
-    "cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc"
+    "disk_size": "100",
+    "cluster_config": "OnDemand bcs.ps.g.large img-ubuntu-vpc"
 }

inputs

@@ -1,7 +1,6 @@
 {
+  "{{ project_name }}.INPUT": {{ INPUT | tojson }},
   "{{ project_name }}.docker": "{{ docker }}",
-  "{{ project_name }}.file": "{{ file }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}"
-}
-
+}

tasks/MD5.wdl

@@ -1,13 +1,16 @@
 task MD5 {
 
-	File file
-	String name = basename(file)
+	Array[File] INPUT
 	String docker
 	String cluster_config
 	String disk_size
 
 	command <<<
-		md5sum ${file} > ${name}.md5
+		for file in ${sep=" " INPUT}
+		do
+			md5sum ${file} > ${file}.md5
+		done
+		cat `ls | grep .md5$` > OUTPUT.md5
 	>>>
 
 	runtime {
@@ -18,6 +21,6 @@ task MD5 {
 	}
 
 	output {
-		File MD5 = "${name}.md5"
+		File MD5 = "OUTPUT.md5"
 	}
 }

workflow.wdl

@@ -1,14 +1,14 @@
 import "./tasks/MD5.wdl" as MD5
 
 workflow {{ project_name }} {
-	File file
+	Array[File] INPUT
 	String docker
 	String cluster_config
 	String disk_size
 
 	call MD5.MD5 as MD5 {
 		input:
-		file = file,
+		INPUT = INPUT,
 		docker = docker,
 		disk_size = disk_size,
 		cluster_config=cluster_config