benchmark

tasks/benchmark.wdl

@@ -28,13 +28,13 @@ task benchmark {
 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.filtered.rtg.vcf.gz
 
 		if [ ${sample_mark} == "LCL5" ];then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL5.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.vcf.gz ${sample}.filtered.rtg.vcf.gz -f ${benchmarking_dir}/LCL5.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 	    elif [ ${sample_mark} == "LCL6" ]; then
-	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL6.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.vcf.gz ${sample}.filtered.rtg.vcf.gz -f ${benchmarking_dir}/LCL6.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
         elif [ ${sample_mark} == "LCL7" ]; then
-        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL7.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.vcf.gz ${sample}.filtered.rtg.vcf.gz -f ${benchmarking_dir}/LCL7.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 	    elif [ ${sample_mark} == "LCL8" ]; then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL8.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.vcf.gz ${sample}.filtered.rtg.vcf.gz -f ${benchmarking_dir}/LCL8.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
         else
         	echo "only for quartet samples"
         fi		
@@ -48,8 +48,8 @@ task benchmark {
 	}
 
 	output {
-		File rtg_vcf = "${sample}.rtg.vcf.gz"
-		File rtg_vcf_index = "${sample}.rtg.vcf.gz.tbi"
+		File rtg_vcf = "${sample}.filtered.rtg.vcf.gz"
+		File rtg_vcf_index = "${sample}.filtered.rtg.vcf.gz.tbi"
 		File gzip_vcf = "${sample}.vcf.gz"
 		File gzip_vcf_index = "${sample}.vcf.gz.tbi"
 		File roc_all_csv = "${sample}.roc.all.csv.gz"