test workflow

tasks/ngscheckmate_fastq.wdl

@@ -1,7 +1,7 @@
 task ngscheckmate_fastq {
-  String sample_id
-  File fastq1
-  File fastq2
+  String output_id
+  File fq1
+  File fq2
   String subsampling_rate
   String docker
   String cluster_config
@@ -12,7 +12,7 @@ task ngscheckmate_fastq {
     set -e
     nt=$(nproc)
     export NCM_HOME=/opt/NGSCheckMate
-    python /opt/NGSCheckMate/ncm_fastq.py -1 ${fastq1} -2 ${fastq2} /opt/NGSCheckMate/SNP/SNP.pt -p $nt -s ${subsampling_rate} > ${sample_id}.vaf
+    python /opt/NGSCheckMate/ncm_fastq.py -1 ${fq1} -2 ${fq2} /opt/NGSCheckMate/SNP/SNP.pt -p $nt -s ${subsampling_rate} > ${output_id}.vaf
   >>>
 
   runtime {
@@ -22,6 +22,6 @@ task ngscheckmate_fastq {
       dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
   }
   output {
-    File vaf="${sample_id}.vaf"
+    File vaf="${output_id}.vaf"
   }
 }

workflow.wdl

@@ -6,16 +6,16 @@ workflow {{ project_name }} {
   Array[File] fastq1
   Array[File] fastq2
   String subsampling_rate
-	String docker
-	String cluster_config
-	String disk_size
+  String docker
+  String cluster_config
+  String disk_size
 
   scatter (idx in range(length(sample_id))) {
     call ngscheckmate_fastq.ngscheckmate_fastq as ngscheckmate_fastq {
       input:
-      sample_id=sample_id[idx],
-      fastq1=fastq1[idx],
-      fastq2=fastq2[idx],
+      output_id=sample_id[idx],
+      fq1=fastq1[idx],
+      fq2=fastq2[idx],
       subsampling_rate=subsampling_rate,
       docker=docker,
       disk_size=disk_size,