update

defaults

@@ -0,0 +1,5 @@
+{
+  "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 }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/ngscheckmate:v1.0.0",
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
   "{{ project_name }}.input_file": "{{ input_file }}",
   "{{ project_name }}.fastq_dir": "{{ fastq_dir }}",
-  "{{ project_name }}.disk_size": "100",
-  "{{ project_name }}.cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc"
+  "{{ project_name }}.docker": "{{ docker }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}"
 }

tasks/NGScheckMates.wdl

@@ -1,4 +1,5 @@
 task NGScheckMates {
+  String sample_id
 	File fastq_dir
 	File input_file
 	String docker
@@ -11,6 +12,12 @@ task NGScheckMates {
 		nt=$(nproc)
 		export NCM_HOME=/opt/NGSCheckMate
 		python /opt/NGSCheckMate/ncm_fastq.py -l ${input_file} -pt /opt/NGSCheckMate/SNP/SNP.pt -O '.' -p $nt -f -s 0.3
+    # rename
+    mv output_all.txt {sample_id}_output_all.txt
+    mv wd.txt {sample_id}_wd.txt
+    mv output_corr_matrix.txt {sample_id}_output_corr_matrix.txt
+    mv output_matched.txt {sample_id}_output_matched.txt
+    mv r_script.r {sample_id}_r_script.r
 	>>>
 
 	runtime {
@@ -20,10 +27,10 @@ task NGScheckMates {
     	dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File all_txt="output_all.txt"
-		File ncm="wd.txt"
-		File cor_txt="output_corr_matrix.txt"
-		File matched_txt="output_matched.txt"
-		File r_script="r_script.r"
+		File all_txt="{sample_id}_output_all.txt"
+		File ncm="{sample_id}_wd.txt"
+		File cor_txt="{sample_id}_output_corr_matrix.txt"
+		File matched_txt="{sample_id}_output_matched.txt"
+		File r_script="{sample_id}_r_script.r"
 	}
 }

workflow.wdl

@@ -1,6 +1,7 @@
 import "./tasks/NGScheckMates.wdl" as NGScheckMates
 
 workflow {{ project_name }} {
+  String sample_id
 	File fastq_dir
 	File input_file
 	String docker
@@ -9,6 +10,7 @@ workflow {{ project_name }} {
 
 	call NGScheckMates.NGScheckMates as NGScheckMates {
 		input:
+    sample_id=sample_id,
 		fastq_dir=fastq_dir,
 		input_file=input_file,
 		docker=docker,