mostly 3 fq to 1 fq

README.md

@@ -1,6 +1,6 @@
-> Author: Yueqiang Song
-> Email: songyq_hello@163.com
-> Last Updates: 25/12/2020
+> Author: Yueqiang Song    
+> Email: songyq_hello@163.com     
+> Last Updates: 25/12/2020    
 
 #### Requirements
 
@@ -18,3 +18,5 @@ $ choppy apps
 ```
 $ choppy batch songyueqiang/mergefq-latest sample.csv --project-name Your_project_name
 ```
+
+

inputs

@@ -1,5 +1,7 @@
 {
-  "{{ project_name }}.fq_list": "{{ fq_list }}",
+  "{{ project_name }}.fq1": "{{ fq1 }}",
+  "{{ project_name }}.fq2": "{{ fq2 }}",
+  "{{ project_name }}.fq3": "{{ fq3 }}",
   "{{ project_name }}.fq_m": "{{ fq_m }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc"

tasks/mergefq.wdl

@@ -1,14 +1,14 @@
 task mergefq {
-	file fq_list
+	File fq1
+	File fq2
+	File fq3
 	String fq_m
 	String disk_size
 	String cluster_config
 
 	command <<<
 		set -euo pipefail
-		cat ${fq_list}|IFS=";" read -a myarray
-        cat ${myarray[@]} >${fq_m}
-		
+	    cat ${fq1} ${fq2} ${fq3} > ${fq_m}
 	>>>
 
 	runtime {

workflow.wdl

@@ -1,15 +1,19 @@
 import "./tasks/mergefq.wdl" as mergefq
 
 workflow {{ project_name }} {
-	File fq_list
+	File fq1
+	File fq2
+	File fq3
 	String fq_m
 	String disk_size
 	String cluster_config
 
 	call mergefq.mergefq as mergefq {
 		input:
-			fq_list=fq_list,
-			fq_m=fq_m,
+			fq1=fq1,
+			fq2=fq2,
+			fq3=fq3,
+			fq_m=fq_m
 			disk_size=disk_size,
 			cluster_config=cluster_config
 	}