first commit

inputs

+{
+  "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
+  "{{ project_name }}.read1": "{{ read1 }}",
+  "{{ project_name }}.disk_size": "150",
+  "{{ project_name }}.read2": "{{ read2 }}",
+  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5"
+}

tasks/fastqc.wdl

+task fastqc {
+	File read
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		fastqc -t $nt -o ./ ${read}
+	>>>
+
+	runtime {
+		docker:docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File fastqc_html = sub(basename(read), "\\.(fastq|fq)\\.gz$", "_fastqc.html")
+		File fastqc_zip = sub(basename(read), "\\.(fastq|fq)\\.gz$", "_fastqc.zip")
+	}
+}

workflow.wdl

+import "./tasks/fastqc.wdl" as fastqc
+
+workflow {{ project_name }}{
+	File read1
+	File read2
+	String docker
+	String cluster_config
+	String disk_size
+
+scatter ( read in [read1, read2]) {
+	call fastqc.fastqc as fastqc {
+		input:
+		read=read,
+		docker=docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+}
+}