first commit

inputs

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

tasks/getBam.wdl

+task getBam {
+	File bam
+	File bam_idx
+	String sample
+	String region
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		/opt/conda/bin/samtools view -b ${bam} "${region}" > ${region}.${sample}.bam
+		/opt/conda/bin/samtools index ${region}.${sample}.bam
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File region_bam = "${region}.${sample}.bam"
+		File region_bai = "${region}.${sample}.bam.bai"
+	}
+}

workflow.wdl

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