cat multiple files to one file

README.md

@@ -1,6 +1,6 @@
 > Author: Jun Shang
 > Email: shangjunv@163.com
-> Last Updates: 22/10/2020
+> Last Updates: 10/05/2022
 
 #### Requirements
 
@@ -16,5 +16,22 @@ $ choppy apps
 #### quick start
 
 ```
-$ choppy batch junshang/catreads-latest sample.csv --project-name Your_project_name
+$ choppy batch junshang/catreads-latest sample.json --project-name Your_project_name
+```
+
+#### Input File
+
+Input file `samples.json` should be in the form of json.
+For example:
+
+```json
+{
+  "fq": [
+    "oss://choppy-cromwell-result/test-choppy/..._lane1_1.fq.gz",
+    "oss://choppy-cromwell-result/test-choppy/..._lane2_1.fq.gz",
+    "oss://choppy-cromwell-result/test-choppy/..._lane3_1.fq.gz"
+  ],
+  "panel_id": "test_1.fq.gz",
+  "sample_id": "test_1.fq.gz"
+}
 ```

inputs

@@ -1,7 +1,6 @@
 {
-  "{{ project_name }}.fq1": "{{ fq1 }}",
-  "{{ project_name }}.fq2": "{{ fq2 }}",
-  "{{ project_name }}.fq3": "{{ fq3 }}",
+  "{{ project_name }}.fq": "{{ fq | tojson }}",
+  "{{ project_name }}.sample_name": "{{ sample_name }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc"
 }

tasks/catreads.wdl

@@ -1,12 +1,14 @@
 task catreads {
-	File fq1
-	File fq2
-	String fq3
+	Array[File] fq
+	String sample_name
 	String disk_size
 	String cluster_config
 
 	command <<<
-		cat ${fq1} ${fq2} > ${fq3}
+	        set -o pipefail
+		    set -e
+
+			cat ${sep=" " fq} > ${sample_name}
 	>>>
 
 	runtime {
@@ -16,6 +18,6 @@ task catreads {
 	}
 
 	output {
-		File merge_fq = "${fq3}"
+		File merge_fq = "${sample_name}"
 	}
 }

workflow.wdl

@@ -2,16 +2,14 @@ import "./tasks/catreads.wdl" as catreads
 
 workflow {{ project_name }} {
 	String disk_size
-	File fq1
-	File fq2
-	String fq3
 	String cluster_config
+	Array[File] fq
+	String sample_name
 
 	call catreads.catreads as catreads {
 		input:
-			fq1=fq1,
-			fq2=fq2,
-			fq3=fq3,
+			fq=fq,
+			sample_name=sample_name,
 			disk_size=disk_size,
 			cluster_config=cluster_config
 	}