first commit

inputs

+{
+  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/ngscheckmate:v1.0.0",
+  "{{ project_name }}.input_file": "{{ input_file }}",
+  "{{ project_name }}.fastq_dir": "{{ fastq_dir }}",
+  "{{ project_name }}.disk_size": "100",
+  "{{ project_name }}.cluster_config": "OnDemand ecs.sn1ne.4xlarge img-ubuntu-vpc"
+}

tasks/NGScheckMates.wdl

+task NGScheckMates {
+	File fastq_dir
+	File input_file
+	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 -l ${input_file} -pt /opt/NGSCheckMate/SNP/SNP.pt -O '.' -p $nt
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk:"cloud_ssd 40"
+    	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"
+	}
+}

workflow.wdl

+import "./tasks/NGScheckMates.wdl" as NGScheckMates
+
+workflow {{ project_name }} {
+	File fastq_dir
+	File input_file
+	String docker
+	String cluster_config
+	String disk_size
+
+	call NGScheckMates.NGScheckMates as NGScheckMates {
+		input:
+		fastq_dir=fastq_dir,
+		input_file=input_file,
+		docker=docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+}