first commit

defaults

@@ -0,0 +1,7 @@
+{
+  "fasta": "GRCh38.d1.vd1.fa",
+  "disk_size": "500",
+  "cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+  "docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
+  "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"
+}

inputs

@@ -0,0 +1,11 @@
+{
+  "{{ project_name }}.fasta": "{{ fasta }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.docker": "{{ docker }}",
+  "{{ project_name }}.bam_index": "{{ bam_index }}",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}",
+  "{{ project_name }}.bam": "{{ bam }}",
+  "{{ project_name }}.memory": "{{ memory }}",
+  "{{ project_name }}.sample": "{{ sample }}",
+  "{{ project_name }}.ref_dir": "{{ ref_dir }}"
+}

tasks/pre.wdl

@@ -0,0 +1,39 @@
+task pre {
+
+    File ref_dir
+	File fasta
+	File vcf
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		mkdir -p /cromwell_root/tmp
+		cp -r ${ref_dir} /cromwell_root/tmp/
+
+		export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa
+
+		if [[ ${sample} =~ "LCL7" ]]; then
+			/opt/hap.py/bin/pre.py ${vcf} ${sample}.vcf.gz -r ${ref_dir}/${fasta} -D -L --fixchr --gender male --threads $nt --logfile ${sample}.vairants.normalization.pre.log
+		else
+			/opt/hap.py/bin/pre.py ${vcf} ${sample}.vcf.gz -r ${ref_dir}/${fasta} -D -L --fixchr --gender female --threads $nt --logfile ${sample}.vairants.normalization.pre.log
+		fi
+
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File normalized_vcf = "${sample}.vcf.gz"
+		File log = "${sample}.vairants.normalization.pre.log"
+	}
+}

workflow.wdl

@@ -0,0 +1,24 @@
+import "./tasks/pre.wdl" as pre
+
+
+workflow {{ project_name }} {
+
+    File ref_dir
+	File fasta
+	File vcf
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+
+	call pre.pre as pre_1 {
+		input:
+		fasta=fasta,
+		ref_dir=ref_dir,
+		vcf=vcf,
+		sample=sample,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+}