first commit

inputs

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+{
+  "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
+  "{{ project_name }}.ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",
+  "{{ project_name }}.fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",
+  "{{ project_name }}.read": "{{ read }}",
+  "{{ project_name }}.disk_size": "100",
+  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0"
+}

tasks/fastq_screen.wdl

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+task fastq_screen {
+	File read
+	File ref_dir
+	File fastq_screen_conf
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		mkdir -p /cromwell_root/tmp
+		cp -r ${ref_dir} /cromwell_root/tmp/
+		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --threads $nt --outdir ./ ${read}
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File png = sub(basename(read), "\\.(fastq|fq)\\.gz$", "_screen.html")
+		File txt = sub(basename(read), "\\.(fastq|fq)\\.gz$", "_screen.png")
+		File html = sub(basename(read), "\\.(fastq|fq)\\.gz$", "_screen.txt")
+	}
+}

workflow.wdl

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+import "./tasks/fastq_screen.wdl" as fastq_screen
+
+workflow {{ project_name }} {
+	File read
+	File ref_dir
+	File fastq_screen_conf
+	String docker
+  	String cluster_config
+  	String disk_size
+
+	call fastq_screen.fastq_screen as fastq_screen {
+		input:
+		read=read,
+		ref_dir=ref_dir,
+		fastq_screen_conf=fastq_screen_conf,
+		docker=docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+}