Add output_id into fastq_ncm.wdl

inputs

@@ -2,6 +2,7 @@
   "{{ project_name }}.sample_id": "{{ sample_id }}",
   "{{ project_name }}.fastq1": {{ fastq1 | tojson }},
   "{{ project_name }}.fastq2": {{ fastq2 | tojson }},
+  "{{ project_name }}.output_id": {{ output_id | tojson }},
   "{{ project_name }}.subsampling_rate": "{{ subsampling_rate }}",
   "{{ project_name }}.docker": "{{ docker }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",

tasks/fastq_ncm.wdl

@@ -2,7 +2,7 @@ task fastq_ncm {
   
   File fq1
   File fq2
-  String output_id=basename(fq1, "_R1.fastq.gz")
+  String output_id
   String subsampling_rate
   String docker
   String cluster_config

workflow.wdl

@@ -6,23 +6,25 @@ workflow {{ project_name }} {
   String sample_id
   Array[File] fastq1
   Array[File] fastq2
+  Array[String] output_id
   String subsampling_rate
   String docker
   String cluster_config
   String disk_size
 
-  scatter (idx in range(length(fastq1))) {
+  scatter (idx in range(length(output_id))) {
     call fastq_ncm.fastq_ncm as fastq_ncm {
       input:
       fq1=fastq1[idx],
       fq2=fastq2[idx],
+      output_id=output_id[idx],
       subsampling_rate=subsampling_rate,
       docker=docker,
       disk_size=disk_size,
       cluster_config=cluster_config
     }
   }
-  
+
   call vaf_ncm.vaf_ncm as vaf_ncm {
     input:
     vaf=fastq_ncm.vaf,