union

tasks/filter_vcf.wdl

+task filter_vcf {
+	
+	File benchmark_region
+	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
+	
+
+	command <<<
+
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${LCL5_vcf} --include-bed=${benchmark_region} -o LCL5.high.confidence.calls.vcf.gz
+
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${LCL6_vcf} --include-bed=${benchmark_region} -o LCL6.high.confidence.calls.vcf.gz
+
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${LCL7_vcf} --include-bed=${benchmark_region} -o LCL7.high.confidence.calls.vcf.gz
+
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${LCL8_vcf} --include-bed=${benchmark_region} -o LCL8.high.confidence.calls.vcf.gz
+
+		>>>
+
+		runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File LCL5_filtered_vcf = "LCL5.high.confidence.calls.vcf.gz"
+		File LCL5_filtered_vcf_idx = "LCL5.high.confidence.calls.vcf.gz.tbi"
+		File LCL6_filtered_vcf = "LCL6.high.confidence.calls.vcf.gz"
+		File LCL6_filtered_vcf_idx = "LCL6.high.confidence.calls.vcf.gz.tbi"
+		File LCL7_filtered_vcf = "LCL7.high.confidence.calls.vcf.gz"
+		File LCL7_filtered_vcf_idx = "LCL7.high.confidence.calls.vcf.gz.tbi"
+		File LCL8_filtered_vcf = "LCL8.high.confidence.calls.vcf.gz"
+		File LCL8_filtered_vcf_idx = "LCL8.high.confidence.calls.vcf.gz.tbi"
+	}
+}
+
+
+
+
+
+
+

tasks/final_merge.wdl

 	File callable_merged_intersect_bed
 	File HR_merged_intersect_bed
 	File variants_merged_bed
+	File 10X_bed
+	File PMRA_bed
 	String docker
 	String disk_size
 	String cluster_config
 
 		/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
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools subtract -a benchmark_regions.bed -b false.positive.bed > benchmark_regions.filtered.bed
+
 		>>>
 
 		runtime {
 
 	output {
 		File variant_invariant = "variant_invariant.bed"
-		File benchmark = "benchmark_regions.bed"
+
+		File benchmark_region = "benchmark_regions.filtered.bed"
 	}
 }