test workflow

tasks/ngscheckmate_fastq.wdl

@@ -1,27 +1,27 @@
 task ngscheckmate_fastq {
   String sample_id
-	File fastq1
-	File fastq1
+  File fastq1
+  File fastq2
   String subsampling_rate
-	String docker
-	String cluster_config
-	String disk_size
+  String docker
+  String cluster_config
+  String disk_size
 
-	command <<<
-		set -o pipefail
-		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} > ${sample_id}.vaf
-	>>>
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(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
+  >>>
 
-	runtime {
-		docker:docker
-    	cluster:cluster_config
-    	systemDisk:"cloud_ssd 40"
-    	dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-	output {
-		File vaf="${sample_id}.vaf"
-	}
+  runtime {
+    docker:docker
+      cluster:cluster_config
+      systemDisk:"cloud_ssd 40"
+      dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  output {
+    File vaf="${sample_id}.vaf"
+  }
 }