revised input

README.md

@@ -8,9 +8,14 @@
 - Ali-Cloud
 
 ```
-$ source activate choppy
+# Activate choppy environment
+$ open-choppy-env
+
+# Install app
 $ choppy install junshang/catreads
-$ choppy apps
+
+# Create input file `samples.json`
+touch samples.json
 ```
 
 #### quick start

inputs

@@ -1,5 +1,5 @@
 {
-  "{{ project_name }}.fq": "{{ fq | tojson }}",
+  "{{ project_name }}.fqs": "{{ fqs | tojson }}",
   "{{ project_name }}.sample_name": "{{ sample_name }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc"

samples.json

@@ -0,0 +1,8 @@
+{
+    "fqs":[
+        "oss://choppy-app-example-data/RNAseq/fastq_1m_reads/tumor_1M_1_R1.fq.gz",
+        "oss://choppy-app-example-data/RNAseq/test_fq/test_R1.fq.gz"
+    ],
+    "sample_name": "test_1.fq.gz",
+    "sample_id": "test_1"
+}

tasks/catreads.wdl

@@ -1,5 +1,5 @@
 task catreads {
-	Array[File] fq
+	Array[File] fqs
 	String sample_name
 	String disk_size
 	String cluster_config
@@ -8,7 +8,7 @@ task catreads {
 	        set -o pipefail
 		    set -e
 
-			cat ${sep=" " fq} > ${sample_name}
+			cat ${sep=" " fqs} > ${sample_name}
 	>>>
 
 	runtime {

workflow.wdl

@@ -3,12 +3,12 @@ import "./tasks/catreads.wdl" as catreads
 workflow {{ project_name }} {
 	String disk_size
 	String cluster_config
-	Array[File] fq
+	Array[File] fqs
 	String sample_name
 
 	call catreads.catreads as catreads {
 		input:
-			fq=fq,
+			fqs=fqs,
 			sample_name=sample_name,
 			disk_size=disk_size,
 			cluster_config=cluster_config