reference dataset4.0

inputs

@@ -1,5 +1,5 @@
 {
-  "{{ project_name }}.benchmarking_dir": "oss://pgx-result/renluyao/manuscript/benchmark_calls_v3.0/",
+  "{{ project_name }}.benchmarking_dir": "oss://pgx-result/renluyao/manuscript_v3.0/reference_dataset_v4.0/",
   "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
   "{{ project_name }}.disk_size": "500",
   "{{ project_name }}.vcf_idx": "{{ vcf_idx }}",

tasks/benchmark.wdl

@@ -3,7 +3,7 @@ task benchmark {
 	File vcf_idx
 	File benchmarking_dir
 	File ref_dir
-	String sample = basename(vcf,".rtg.vcf.gz")
+	String sample
 	String fasta
 	String docker
 	String cluster_config
@@ -20,13 +20,13 @@ task benchmark {
 		export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa
 
 		if [[ ${sample} =~ "LCL5" ]];then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.afterfilterdiffbed.vcf.gz ${vcf} -f ${benchmarking_dir}/LCL5.high.confidence.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.voted.mendelian.vcf.gz ${vcf} -f ${benchmarking_dir}/LCL5.highconfidence.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 	    elif [[ ${sample} =~ "LCL6" ]]; then
-	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.afterfilterdiffbed.vcf.gz ${vcf} -f ${benchmarking_dir}/LCL6.high.confidence.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.voted.mendelian.vcf.gz ${vcf} -f ${benchmarking_dir}/LCL6.highconfidence.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
         elif [[ ${sample} =~ "LCL7" ]]; then
-        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.afterfilterdiffbed.vcf.gz ${vcf} -f ${benchmarking_dir}/LCL7.high.confidence.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.voted.mendelian.vcf.gz ${vcf} -f ${benchmarking_dir}/LCL7.highconfidence.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 	    elif [[ ${sample} =~ "LCL8" ]]; then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.afterfilterdiffbed.vcf.gz ${vcf} -f ${benchmarking_dir}/LCL8.high.confidence.bed.gz --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.voted.mendelian.vcf.gz ${vcf} -f ${benchmarking_dir}/LCL8.highconfidence.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
         else
         	echo "only for quartet samples"
         fi		

workflow.wdl

@@ -5,6 +5,7 @@ workflow {{ project_name }} {
 	File vcf_idx
 	File benchmarking_dir
 	File ref_dir
+	String sample
 	String fasta
 	String docker
 	String cluster_config
@@ -16,6 +17,7 @@ workflow {{ project_name }} {
 		vcf_idx=vcf_idx,
 		benchmarking_dir=benchmarking_dir,
 		ref_dir=ref_dir,
+		sample=sample,
 		fasta=fasta,
 		docker=docker,
 		cluster_config=cluster_config,