first commit

inputs

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+{
+  "{{ project_name }}.out_dir": "String (optional, default = \"./\")",
+  "{{ 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": "{{ disk_size }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}"
+}

tasks/NGScheckMates.wdl

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+task NGScheckMates {
+	File fastq_dir
+	File input_file
+	File out_dir
+	String docker
+	String out_dir = "./"
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		python ncm_fastq.py -l ${input_file} -pt SNP/SNP.pt –O ${out_dir} -p $nt -s 0.3 -f
+	>>>
+
+	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 cor_txt="output_corr_matrix.txt"
+		File matched_txt="output_matched.txt"
+		File r_script="r_script.r"
+	}
+}

workflow.wdl

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