first commit

defaults

+{
+    "docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bamreadcount:v0.8.0",
+    "disk_size": "200",
+    "cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc"
+}

inputs

+{
+  "{{ project_name }}.docker": "{{ docker }}",
+  "{{ project_name }}.reference": "{{ reference }}",
+  "{{ project_name }}.bedfile": "{{ bedfile }}",
+  "{{ project_name }}.bamfile": "{{ bamfile }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}",
+  "{{ project_name }}.sample_id": "{{ sample_id }}"
+}
+

tasks/BAMReadCount.wdl

+task BAMReadCount {
+
+	String sample_id
+	File reference
+	File bedfile
+	File bamfile
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		bam-readcount -f ${reference} -l ${bedfile} ${bamfile} > ${sample_id}.readcount
+	>>>
+
+	runtime {
+		docker: docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File BAMReadCount = "${sample_id}.readcount"
+	}
+}

workflow.wdl

+import "./tasks/BAMReadCount.wdl" as BAMReadCount
+
+workflow {{ project_name }} {
+	File reference
+	File bamfile
+	String sample_id
+	String docker
+	String cluster_config
+	String disk_size
+	Int number
+
+	call BAMReadCount.BAMReadCount as BAMReadCount {
+		input:
+		reference = reference,
+		bamfile = bamfile,
+		docker = docker,
+		disk_size = disk_size,
+		cluster_config=cluster_config,
+		sample_id=sample_id,
+		number=number
+	}
+}