benchmark file name

inputs

 {
-  "{{ project_name }}.benchmarking_dir": "oss://pgx-result/renluyao/high_confidence_call/20200125_high_confidence_call_33vcf_final/",
+  "{{ project_name }}.benchmarking_dir": "oss://chinese-quartet/quartet-result-data/NCTR_benchmarking_20181215/",
   "{{ project_name }}.vcfstat.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
   "{{ project_name }}.qualimap.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
   "{{ project_name }}.qualimap.cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",

tasks/benchmark.wdl

 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.rtg.vcf.gz
 
 		if [ ${sample_mark} == "LCL5" ];then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.consensus.vcf.gz ${sample}.rtg.vcf.gz --threads $nt -o ${sample}
+			/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}
 	    elif [ ${sample_mark} == "LCL6" ]; then
-	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.consensus.vcf.gz ${sample}.rtg.vcf.gz --threads $nt -o ${sample}
+	    	/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}
         elif [ ${sample_mark} == "LCL7" ]; then
-        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.consensus.vcf.gz ${sample}.rtg.vcf.gz --threads $nt -o ${sample}
+        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL6.bed.gz --threads $nt -o ${sample}
 	    elif [ ${sample_mark} == "LCL8" ]; then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.consensus.vcf.gz ${sample}.rtg.vcf.gz --threads $nt -o ${sample}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/LCL6.bed.gz --threads $nt -o ${sample}
         else
         	echo "only for quartet samples"
         fi		

tasks/sentieon.wdl

 		set -o pipefail
 		set -e
 		cat ${aln_metrics} | sed -n '2,2p'  > aln_metrics.header
-		cat ${aln_metrics} | sed -n '3,3p'  > ${sample_name}.aln_metrics
+		cat ${aln_metrics} | sed -n '5,5p'  > ${sample_name}.aln_metrics
 		cat ${dedup_metrics} | sed -n '2,2p' > dedup_metrics.header
 		cat ${dedup_metrics} | sed -n '3,3p' > ${sample_name}.dedup_metrics
 		cat ${is_metrics} | sed -n '2,2p' > is_metrics.header