test workflow

inputs

@@ -1,7 +1,7 @@
 {
-  "{{ project_name }}.sample_id": "{{ sample_id }}",
-  "{{ project_name }}.fastq1": "{{ fastq1 }}",
-  "{{ project_name }}.fastq2": "{{ fastq2 }}",
+  "{{ project_name }}.sample_id": {{ sample_id | tojson }},
+  "{{ project_name }}.fastq1": {{ fastq1 | tojson }},
+  "{{ project_name }}.fastq2": {{ fastq2 | tojson }},
   "{{ project_name }}.subsampling_rate": "{{ subsampling_rate }}",
   "{{ project_name }}.docker": "{{ docker }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",

workflow.wdl

@@ -2,23 +2,20 @@ import "./tasks/ngscheckmate_fastq.wdl" as ngscheckmate_fastq
 
 workflow {{ project_name }} {
   
-  String sample_id
-	File fastq1
-	File fastq2
+  Array[String] sample_id
+  Array[File] fastq1
+  Array[File] fastq2
   String subsampling_rate
 	String docker
 	String cluster_config
 	String disk_size
 
-  Array[File] fastq1_arr = fastq1
-  Array[File] fastq2_arr = fastq2
-
-  scatter (idx in range(length(fastq1_arr))) {
+  scatter (idx in range(length(sample_id))) {
     call ngscheckmate_fastq.ngscheckmate_fastq as ngscheckmate_fastq {
       input:
-      sample_id=sample_id,
-      fastq1=fastq1_arr[idx],
-      fastq2=fastq2_arr[idx],
+      sample_id=sample_id[idx],
+      fastq1=fastq1[idx],
+      fastq2=fastq2[idx],
       subsampling_rate=subsampling_rate,
       docker=docker,
       disk_size=disk_size,