first commit

defaults

+{
+    "disk_size": "100",
+    "cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
+    "samtools_docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1"
+}

inputs

+{
+  "{{ project_name }}.bam": "{{ bam }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.samtools_docker": "{{ samtools_docker }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}"
+}

tasks/index.wdl

+task depth {
+	File bam
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		samtools index ${bam}
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File bai = "${bam}.bai"
+	}
+}

workflow.wdl

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