vcf

inputs

@@ -1,17 +1,28 @@
 {
+  "{{ project_name }}.LCL5_vcf": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL5.voted.mendelian.vcf.gz",
   "{{ project_name }}.LCL8_callable_bed": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL8.consensus.merged.bed",
   "{{ project_name }}.LCL6_variants_bed": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL6.variants.bed",
+  "{{ project_name }}.LCL6_vcf_idx": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL6.voted.mendelian.vcf.gz.tbi",
   "{{ project_name }}.LCL5_variants_bed": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL5.variants.bed",
   "{{ project_name }}.LCL8_HR_bed": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL8.27.homo_ref.consensus.bed",
   "{{ project_name }}.disk_size": "150",
   "{{ project_name }}.LCL7_variants_bed": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL7.variants.bed",
   "{{ project_name }}.LCL7_callable_bed": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL7.consensus.merged.bed",
+  "{{ project_name }}.filter_vcf.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
   "{{ project_name }}.docker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
   "{{ project_name }}.LCL5_HR_bed": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL5.27.homo_ref.consensus.bed",
+  "{{ project_name }}.LCL6_vcf": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL6.voted.mendelian.vcf.gz",
   "{{ project_name }}.LCL7_HR_bed": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL7.27.homo_ref.consensus.bed",
   "{{ project_name }}.LCL5_callable_bed": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL5.consensus.merged.bed",
+  "{{ project_name }}.LCL7_vcf": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL7.voted.mendelian.vcf.gz",
   "{{ project_name }}.LCL6_callable_bed": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL6.consensus.merged.bed",
+  "{{ project_name }}.LCL5_vcf_idx": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL5.voted.mendelian.vcf.gz.tbi",
+  "{{ project_name }}.PMRA_bed": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/annotated.notValidatedIGV.vcf.bed",
   "{{ project_name }}.LCL8_variants_bed": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL8.variants.bed",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
-  "{{ project_name }}.LCL6_HR_bed": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL6.27.homo_ref.consensus.bed"
-}
+  "{{ project_name }}.LCL8_vcf_idx": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL8.voted.mendelian.vcf.gz.tbi",
+  "{{ project_name }}.LCL8_vcf": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL8.voted.mendelian.vcf.gz",
+  "{{ project_name }}.LCL7_vcf_idx": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL7.voted.mendelian.vcf.gz.tbi",
+  "{{ project_name }}.LCL6_HR_bed": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/LCL6.27.homo_ref.consensus.bed",
+  "{{ project_name }}.bed_10X": "oss://pgx-result/renluyao/manuscript_v3.0/benchmark_region/dat/linked.10x.26559.removed.vcf.bed"
+}

tasks/final_merge.wdl

@@ -3,7 +3,7 @@ task final_merge {
 	File callable_merged_intersect_bed
 	File HR_merged_intersect_bed
 	File variants_merged_bed
-	File 10X_bed
+	File bed_10X
 	File PMRA_bed
 	String docker
 	String disk_size
@@ -16,7 +16,7 @@ task final_merge {
 
 		/opt/ccdg/bedtools-2.27.1/bin/bedtools intersect -a variant_invariant.bed -b ${callable_merged_intersect_bed} > benchmark_regions.bed
 
-		cat ${10X_bed} ${PMRA_bed} | cut -f1,14,15 | sort -k1,1 -k2,2n > false.positive.bed
+		cat ${bed_10X} ${PMRA_bed} | cut -f1,14,15 | sort -k1,1 -k2,2n > false.positive.bed
 
 		/opt/ccdg/bedtools-2.27.1/bin/bedtools subtract -a benchmark_regions.bed -b false.positive.bed > benchmark_regions.filtered.bed
 
@@ -31,7 +31,6 @@ task final_merge {
 
 	output {
 		File variant_invariant = "variant_invariant.bed"
-
 		File benchmark_region = "benchmark_regions.filtered.bed"
 	}
 }

workflow.wdl

@@ -2,6 +2,7 @@ import "./tasks/callable_loci.wdl" as callable_loci
 import "./tasks/final_merge.wdl" as final_merge
 import "./tasks/homo_bed.wdl" as homo_bed
 import "./tasks/variant_bed.wdl" as variant_bed
+import "./tasks/filter_vcf.wdl" as filter_vcf
 
 
 
@@ -19,6 +20,16 @@ workflow {{ project_name }} {
 	File LCL6_variants_bed
 	File LCL7_variants_bed
 	File LCL8_variants_bed
+	File bed_10X
+	File PMRA_bed
+	File LCL5_vcf
+	File LCL6_vcf
+	File LCL7_vcf
+	File LCL8_vcf
+	File LCL5_vcf_idx
+	File LCL6_vcf_idx
+	File LCL7_vcf_idx
+	File LCL8_vcf_idx
 	String docker
 	String disk_size
 	String cluster_config
@@ -61,10 +72,27 @@ workflow {{ project_name }} {
 		callable_merged_intersect_bed=callable_loci.callable_merged_intersect_bed,
 		HR_merged_intersect_bed=homo_bed.HR_merged_intersect_bed,
 		variants_merged_bed=variant_bed.variants_merged_bed,
+		bed_10X=bed_10X,
+		PMRA_bed=PMRA_bed,
 		docker=docker,
 		disk_size=disk_size,
 		cluster_config=cluster_config
 	}
 
+	call filter_vcf.filter_vcf as filter_vcf {
+		input:
+		benchmark_region=final_merge.benchmark_region,
+		LCL5_vcf=LCL5_vcf,
+		LCL6_vcf=LCL6_vcf,
+		LCL7_vcf=LCL7_vcf,
+		LCL8_vcf=LCL8_vcf,
+		LCL5_vcf_idx=LCL5_vcf_idx,
+		LCL6_vcf_idx=LCL6_vcf_idx,	
+		LCL7_vcf_idx=LCL7_vcf_idx,
+		LCL8_vcf_idx=LCL8_vcf_idx,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+
 }