test workflow

defaults

@@ -1,4 +1,5 @@
 {
+  "subsampling_rate": "0.3",
   "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
   "disk_size": "100",
   "docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/ngscheckmate:v1.0.0"

inputs

@@ -1,7 +1,8 @@
 {
   "{{ project_name }}.sample_id": "{{ sample_id }}",
-  "{{ project_name }}.input_file": "{{ input_file }}",
-  "{{ project_name }}.fastq_dir": "{{ fastq_dir }}",
+  "{{ project_name }}.fastq1": "{{ fastq1 }}",
+  "{{ project_name }}.fastq2": "{{ fastq2 }}",
+  "{{ project_name }}.subsampling_rate": "{{ subsampling_rate }}",
   "{{ project_name }}.docker": "{{ docker }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}"

tasks/ngscheckmate_fastq.wdl

@@ -0,0 +1,27 @@
+task ngscheckmate_fastq {
+  String sample_id
+	File fastq1
+	File fastq1
+  String subsampling_rate
+	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} > ${sample_id}.vaf
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk:"cloud_ssd 40"
+    	dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File vaf="${sample_id}.vaf"
+	}
+}

tasks/NGScheckMates.wdl → tasks/vaf_ncm.wdl

@@ -1,4 +1,4 @@
-task NGScheckMates {
+task ngscheckmate_fastq {
   String sample_id
 	File fastq_dir
 	File input_file

workflow.wdl

@@ -1,20 +1,28 @@
-import "./tasks/NGScheckMates.wdl" as NGScheckMates
+import "./tasks/ngscheckmate_fastq.wdl" as ngscheckmate_fastq
 
 workflow {{ project_name }} {
+  
   String sample_id
-	File fastq_dir
-	File input_file
+	File fastq1
+	File fastq2
+  String subsampling_rate
 	String docker
 	String cluster_config
 	String disk_size
 
-	call NGScheckMates.NGScheckMates as NGScheckMates {
-		input:
-    sample_id=sample_id,
-		fastq_dir=fastq_dir,
-		input_file=input_file,
-		docker=docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
+  Array[File] fastq1_arr = fastq1
+  Array[File] fastq2_arr = fastq2
+
+  scatter (idx in range(length(fastq1_arr))) {
+    call ngscheckmate_fastq.ngscheckmate_fastq as ngscheckmate_fastq {
+      input:
+      sample_id=sample_id,
+      fastq1=fastq1_arr[idx],
+      fastq2=fastq2_arr[idx],
+      subsampling_rate=subsampling_rate,
+      docker=docker,
+      disk_size=disk_size,
+      cluster_config=cluster_config
+    }
+  }
 }