first commit

inputs

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+{
+  "{{ project_name }}.depth.disk_size": "500",
+  "{{ project_name }}.chromosome": "{{ chromosome }}",
+  "{{ project_name }}.sample_name": "{{ sample_name }}",
+  "{{ project_name }}.depth.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
+  "{{ project_name }}.bam_index": "{{ bam_index }}",
+  "{{ project_name }}.bam": "{{ bam }}",
+  "{{ project_name }}.depth.cluster_config": "OnDemand bcs.es.c.8xlarge img-ubuntu-vpc"
+}

tasks/depth.wdl

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+task depth {
+	
+	File bam
+	File bam_index
+	String chromosome
+	String sample_name
+	String docker
+	String disk_size
+	String cluster_config
+	
+
+	command <<<
+
+		set -o pipefail
+		set -e
+
+		/opt/conda/bin/samtools depth ${bam} -r ${chromosome} > ${sample_name}.depth.txt
+
+		>>>
+
+		runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File depth = "${sample_name}.depth.txt"
+	}
+}
+
+
+
+

workflow.wdl

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+import "./tasks/depth.wdl" as depth
+
+workflow {{ project_name }} {
+
+	File bam
+	File bam_index
+	String chromosome
+	String sample_name
+
+	
+	call depth.depth as depth {
+		input: 
+		bam=bam,
+		bam_index=bam_index,
+		chromosome=chromosome,
+		sample_name=sample_name
+	}
+
+}
+