first commit

inputs

+{
+  "{{ project_name }}.qualimap.out_dir": "String (optional, default = \"./\")",
+  "{{ project_name }}.cluster_config": "OnDemand ecs.sn1ne.4xlarge img-ubuntu-vpc",
+  "{{ project_name }}.bam": "{{ bam }}",
+  "{{ project_name }}.bed": "{{ bed }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0"
+}

tasks/qualimap.wdl

+task qualimap {
+	File bam
+	File bed
+	String docker
+	String out_dir = "./"
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		/opt/qualimap/qualimap bamqc -bam ${bam} -gff ${bed} -nt $nt -outdir ${out_dir} --java-mem-size=16G
+	>>>
+
+	runtime {
+		docker:docker
+		cluster:cluster_config
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File qualimap_txt = "genome_results.txt"
+		File qualimap_images = "images_qualimapReport"
+		File qualimap_html = "qualimapReport.html"
+		File qulimap_raw_data = "raw_data_qualimapReport"
+	}
+}

workflow.wdl

+import "./tasks/qualimap.wdl" as qualimap
+
+workflow {{ project_name }} {
+	File bam
+	File bed
+	String docker
+	String cluster_config
+	String disk_size
+
+	call qualimap.qualimap as qualimap {
+		input:
+		bam=bam,
+		bed=bed,
+		docker=docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+}