first commit

defaults

+{
+    "regions": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/SureSelect_Human_All_Exon_V6_r2.bed",
+    "disk_size": "100",
+    "cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
+    "docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1"
+}

inputs

+{
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.bam": "{{ bam }}",
+  "{{ project_name }}.bam_idx": "{{ bam_idx }}",
+  "{{ project_name }}.regions": "{{ regions }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.docker": "{{ docker }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}"
+}

tasks/depth.wdl

+task depth {
+	File bam
+	File bam_idx
+	String sample_id
+	String regions
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		/opt/conda/bin/samtools depth -b ${regions} ${bam} > ${sample_id}.depth
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File bam_depth = "${sample_id}.depth"
+	}
+}

workflow.wdl

+import "./tasks/depth.wdl" as depth
+
+
+workflow {{ project_name }} {
+	File bam
+	File bam_idx
+	String sample_id
+	File regions
+	String docker
+	String cluster_config
+	String disk_size
+
+	call depth.depth as depth {
+		input:	
+		bam=bam,
+		bam_idx=bam_idx,
+		sample_id=sample_id,
+		regions=regions,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+}