merge mendelian

inputs

@@ -6,8 +6,10 @@
   "{{ project_name }}.mendelian.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",
   "{{ project_name }}.disk_size": "150",
   "{{ project_name }}.LCL5_benchmark_call": "oss://pgx-result/renluyao/manuscript/benchmark_calls_v3.0/LCL5.afterfilterdiffbed.vcf.gz",
+  "{{ project_name }}.merge_mendelian.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.4",
   "{{ project_name }}.chromo": "{{ chromo }}",
   "{{ project_name }}.LCL5_info_dir": "oss://pgx-result/renluyao/manuscript/20200320_high_confidence_call_intergration/vcf_info/",
   "{{ project_name }}.cluster_config": "OnDemand bcs.b4.xlarge img-ubuntu-vpc",
   "{{ project_name }}.ref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/"
 }
+

tasks/merge_mendelian.wdl

@@ -0,0 +1,26 @@
+task merge_mendelian {
+	File D5_trio_vcf
+	File D6_trio_vcf
+	File consensus_vcf
+	String chromo
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+		cat ${D5_trio_vcf} | grep -v '##' > ${chromo}.D5.txt
+		cat ${D6_trio_vcf} | grep -v '##' > ${chromo}.D6.txt
+		cat ${consensus_vcf} | grep -v '##' > ${chromo}.consensus.txt
+		python /opt/merge_two_family_with_genotype.py -LCL5 ${chromo}.D5.txt -LCL6 ${chromo}.D6.txt -genotype ${chromo}.consensus.txt -family ${chromo}.mendelian
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File chromo_mendelian = "${chromo}.mendelian.txt"
+	}
+}

workflow.wdl

@@ -1,6 +1,7 @@
 import "./tasks/replicate_consensus.wdl" as replicate_consensus
 import "./tasks/mendelian.wdl" as mendelian
 import "./tasks/filtered_benchmark.wdl" as filtered_benchmark
+import "./tasks/merge_mendelian.wdl" as merge_mendelian
 
 workflow {{ project_name }} {
 	File ref_dir
@@ -29,7 +30,7 @@ workflow {{ project_name }} {
 		cluster_config=cluster_config,
 		disk_size=disk_size
 	}
-	call filtered_benchmark.filtered_benchmark as filtered_benchmark{
+	call filtered_benchmark.filtered_benchmark as filtered_benchmark {
 		input:
 		chromo_consensus=replicate_consensus.chromo_consensus,
 		LCL5_info_dir=LCL5_info_dir,
@@ -38,4 +39,13 @@ workflow {{ project_name }} {
 		cluster_config=cluster_config,
 		disk_size=disk_size
 	}
+	call merge_mendelian.merge_mendelian as merge_mendelian {
+		input:
+		D5_trio_vcf=mendelian.D5_trio_vcf,
+		D6_trio_vcf=mendelian.D6_trio_vcf,
+		consensus_vcf=replicate_consensus.consensus_vcf,
+		chromo=chromo,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
 }