first commit

inputs

+{
+  "{{ project_name }}.gvcf": "{{ gvcf }}",
+  "{{ project_name }}.disk_size": "100",
+  "{{ project_name }}.chromo": "{{ chromo }}",
+  "{{ project_name }}.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.1",
+  "{{ project_name }}.cluster_config": "OnDemand bcs.b4.xlarge img-ubuntu-vpc"
+}

tasks/split_gvcf_files.wdl

+task split_gvcf_files {
+	File gvcf
+	String chromo
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+
+		cat ${gvcf} | grep '#CHROM' | sed s'/\t/\n/g' > name
+
+		sed -i '1,9d' name
+
+		for i in {10..133};  do  cat ${gvcf}| cut -f1-9,$i > $i.splited.vcf; done
+
+		ls *splited.vcf | paste - name > rename
+
+		cat rename | while read a b; do mv $a $b.${chromo}.vcf; done
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		Array[File] splited_vcf = glob("*.${chromo}.vcf")
+	}
+}

workflow.wdl

+import "./tasks/split_gvcf_files.wdl" as split_gvcf_files
+
+
+workflow {{ project_name }} {
+	File gvcf
+	String chromo
+	String docker
+	String cluster_config
+	String disk_size
+
+	call split_gvcf_files.split_gvcf_files as split_gvcf_files {
+		input:
+		gvcf=gvcf,
+		chromo=chromo,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+}