scatter

defaults

@@ -0,0 +1,14 @@
+{
+  "benchmarking_dir": "oss://pgx-result/renluyao/manuscript_v3.0/reference_datasets_v202103/",
+  "fasta": "GRCh38.d1.vd1.fa",
+  "BENCHMARKdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
+  "BEDTOOLSdocker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
+  "disk_size": "500",
+  "SMALLcluster_config": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",
+  "bed": "{{ bed }}",
+  "BIGcluster_config": "OnDemand bcs.ps.g.2xlarge img-ubuntu-vpc",
+  "benchmark_region": "oss://pgx-result/renluyao/manuscript_v3.0/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed",
+  "MENDELIANdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",
+  "DIYdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.4",
+  "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"
+}

inputs

@@ -1,24 +1,16 @@
 {
-  "{{ project_name }}.benchmarking_dir": "oss://pgx-result/renluyao/manuscript_v3.0/reference_datasets_v202103/",
-  "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
-  "{{ project_name }}.BENCHMARKdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
-  "{{ project_name }}.LCL6_1": "{{ LCL6_1 }}",
-  "{{ project_name }}.LCL5_3": "{{ LCL5_3 }}",
-  "{{ project_name }}.LCL8_2": "{{ LCL8_2 }}",
-  "{{ project_name }}.disk_size": "500",
-  "{{ project_name }}.LCL8_1": "{{ LCL8_1 }}",
-  "{{ project_name }}.LCL6_3": "{{ LCL6_3 }}",
+  "{{ project_name }}.benchmarking_dir": "{{ benchmarking_dir }}",
+  "{{ project_name }}.fasta": "{{ fasta }}",
+  "{{ project_name }}.BENCHMARKdocker": "{{ BENCHMARKdocker }}",
+  "{{ project_name }}.BEDTOOLSdocker": "{{ BEDTOOLSdocker }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
   "{{ project_name }}.project": "{{ project }}",
-  "{{ project_name }}.LCL7_3": "{{ LCL7_3 }}",
-  "{{ project_name }}.LCL5_1": "{{ LCL5_1 }}",
-  "{{ project_name }}.SMALLcluster_config": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",
-  "{{ project_name }}.LCL6_2": "{{ LCL6_2 }}",
-  "{{ project_name }}.BIGcluster_config": "OnDemand bcs.ps.g.2xlarge img-ubuntu-vpc",
-  "{{ project_name }}.LCL7_2": "{{ LCL7_2 }}",
-  "{{ project_name }}.LCL5_2": "{{ LCL5_2 }}",
-  "{{ project_name }}.LCL7_1": "{{ LCL7_1 }}",
-  "{{ project_name }}.MENDELIANdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",
-  "{{ project_name }}.LCL8_3": "{{ LCL8_3 }}",
-  "{{ project_name }}.DIYdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.4",
-  "{{ project_name }}.ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"
+  "{{ project_name }}.SMALLcluster_config": "{{ SMALLcluster_config }}",
+  "{{ project_name }}.bed": "{{ bed }}",
+  "{{ project_name }}.BIGcluster_config": "{{ BIGcluster_config }}",
+  "{{ project_name }}.benchmark_region": "{{ benchmark_region }}",
+  "{{ project_name }}.MENDELIANdocker": "{{ MENDELIANdocker }}",
+  "{{ project_name }}.DIYdocker": "{{ DIYdocker }}",
+  "{{ project_name }}.ref_dir": "{{ ref_dir }}"
 }

tasks/benchmark.wdl

@@ -2,6 +2,7 @@ task benchmark {
 	File vcf
 	File benchmarking_dir
 	File ref_dir
+	File filtered_bed
 	String sample = basename(vcf,".vcf")
 	String fasta
 	String docker
@@ -25,28 +26,28 @@ task benchmark {
 		echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL8" > LCL8_name
 
 		if [[ ${sample} =~ "LCL5" ]];then
-			/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL5.high.confidence.calls.vcf ${vcf} -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL5.high.confidence.calls.vcf ${vcf} -f ${filtered_bed} --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 			cat ${vcf} | grep '##' > header
 			cat ${vcf} | grep -v '#' > body
 			cat header LCL5_name body > LCL5.vcf
 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip LCL5.vcf -c > ${sample}.reformed.vcf.gz
 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.reformed.vcf.gz
 	    elif [[ ${sample} =~ "LCL6" ]]; then
-	    	/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL6.high.confidence.calls.vcf ${vcf} -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+	    	/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL6.high.confidence.calls.vcf ${vcf} -f ${filtered_bed} --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 			cat ${vcf} | grep '##' > header
 			cat ${vcf} | grep -v '#' > body
 			cat header LCL6_name body > LCL6.vcf
 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip LCL6.vcf -c > ${sample}.reformed.vcf.gz
 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.reformed.vcf.gz
         elif [[ ${sample} =~ "LCL7" ]]; then
-        	/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL7.high.confidence.calls.vcf ${vcf} -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+        	/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL7.high.confidence.calls.vcf ${vcf} -f ${filtered_bed} --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 			cat ${vcf} | grep '##' > header
 			cat ${vcf} | grep -v '#' > body
 			cat header LCL7_name body > LCL7.vcf
 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip LCL7.vcf -c > ${sample}.reformed.vcf.gz
 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.reformed.vcf.gz
 	    elif [[ ${sample} =~ "LCL8" ]]; then
-			/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL8.high.confidence.calls.vcf ${vcf} -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL8.high.confidence.calls.vcf ${vcf} -f ${filtered_bed} --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 			cat ${vcf} | grep '##' > header
 			cat ${vcf} | grep -v '#' > body
 			cat header LCL8_name body > LCL8.vcf

tasks/filter_bed.wdl

@@ -0,0 +1,23 @@
+ task filter_bed {
+	File bed
+	File benchmark_region
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+	
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools intersect -a ${benchmark_region} -b ${bed} > benchmark_region_query_bed.bed
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File filtered_bed = "benchmark_region_query_bed.bed"
+	}
+}

tasks/quartet_mendelian.wdl

@@ -1,26 +1,16 @@
 task quartet_mendelian {
-	File summary_1
-	File summary_2
-	File summary_3
-	File LCL5_hap_1
-	File LCL5_hap_2
-	File LCL5_hap_3
-	File LCL6_hap_1
-	File LCL6_hap_2
-	File LCL6_hap_3
-	File LCL7_hap_1
-	File LCL7_hap_2
-	File LCL7_hap_3	
-	File LCL8_hap_1
-	File LCL8_hap_2
-	File LCL8_hap_3
+	Array[File] summary
+	Array[File] LCL5_hap
+	Array[File] LCL6_hap
+	Array[File] LCL7_hap
+	Array[File] LCL8_hap
 	String docker
 	String project
 	String cluster_config
 	String disk_size
 
 	command <<<
-		cat ${summary_1} ${summary_2} ${summary_3} | grep -v 'Family'> mendelian.summary
+		cat ${sep=" " summary} | grep -v 'Family'> mendelian.summary
 		sed '1iFamily\tTotal_Variants\tMendelian_Concordant_Variants\tMendelian_Concordance_Rate' mendelian.summary > mendelian.txt
 
 		cat mendelian.txt | grep 'INDEL' | cut -f4 | grep -v 'Mendelian_Concordance_Rate' | awk '{for(i=1;i<=NF;i++) {sum[i] += $i; sumsq[i] += ($i)^2}} 
@@ -33,7 +23,7 @@ task quartet_mendelian {
           printf "%f %f \n", sum[i]/NR, sqrt((sumsq[i]-sum[i]^2/NR)/NR)}
          }' >> quartet_snv_aver-std.txt
 
-		cat ${LCL5_hap_1} ${LCL5_hap_2} ${LCL5_hap_3} ${LCL6_hap_1} ${LCL6_hap_2} ${LCL6_hap_3} ${LCL7_hap_1} ${LCL7_hap_2} ${LCL7_hap_3} ${LCL8_hap_1} ${LCL8_hap_2} ${LCL8_hap_3} | grep ALL | sed s'/,/\t/g' > hap.summary
+		cat ${sep=" " LCL5_hap} ${sep=" " LCL6_hap} ${sep=" " LCL7_hap} ${sep=" " LCL8_hap} | grep ALL | sed s'/,/\t/g' > hap.summary
 		sed '1i\Type\tFilter\tTRUTH.TOTAL\tTRUTH.TP\tTRUTH.FN\tQUERY.TOTAL\tQUERY.FP\tQUERY.UNK\tFP.gt\tMETRIC.Recall\tMETRIC.Precision\tMETRIC.Frac_NA\tMETRIC.F1_Score\tTRUTH.TOTAL.TiTv_ratio\tQUERY.TOTAL.TiTv_ratio\tTRUTH.TOTAL.het_hom_ratio\tQUERY.TOTAL.het_hom_ratio' hap.summary > precision_recall
 
 		python /opt/hap_summary.py -hap precision_recall -name ${project}

workflow.wdl

@@ -1,34 +1,25 @@
 import "./tasks/benchmark.wdl" as benchmark
+import "./tasks/filter_bed.wdl" as filter_bed
 import "./tasks/mendelian.wdl" as mendelian
 import "./tasks/merge_mendelian.wdl" as merge_mendelian
 import "./tasks/merge_family.wdl" as merge_family
 import "./tasks/quartet_mendelian.wdl" as quartet_mendelian
 
+workflow project_name {
 
-workflow {{ project_name }} {
-
-	File LCL5_1
-	File LCL6_1
-	File LCL7_1
-	File LCL8_1
-
-	File LCL5_2
-	File LCL6_2
-	File LCL7_2
-	File LCL8_2
-
-	File LCL5_3
-	File LCL6_3
-	File LCL7_3
-	File LCL8_3
+	File inputSamplesFile
+	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
 
 	String BENCHMARKdocker
 	String MENDELIANdocker
 	String DIYdocker
+	String BEDTOOLSdocker
 
 
 	String fasta
 	File ref_dir
+	File benchmark_region
+	File bed
 
 	File benchmarking_dir
 
@@ -38,267 +29,112 @@ workflow {{ project_name }} {
 	String BIGcluster_config
 	String SMALLcluster_config
 
-	call benchmark.benchmark as LCL5_1_benchmark {
-		input:
-		vcf=LCL5_1,
-		benchmarking_dir=benchmarking_dir,
-		ref_dir=ref_dir,
-		fasta=fasta,
-		docker=BENCHMARKdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size,
-	}
-
-	call benchmark.benchmark as LCL5_2_benchmark {
-		input:
-		vcf=LCL5_2,
-		benchmarking_dir=benchmarking_dir,
-		ref_dir=ref_dir,
-		fasta=fasta,
-		docker=BENCHMARKdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size,
-	}
-
-	call benchmark.benchmark as LCL5_3_benchmark {
-		input:
-		vcf=LCL5_3,
-		benchmarking_dir=benchmarking_dir,
-		ref_dir=ref_dir,
-		fasta=fasta,
-		docker=BENCHMARKdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size,
-	}
-
-	call benchmark.benchmark as LCL6_1_benchmark {
-		input:
-		vcf=LCL6_1,
-		benchmarking_dir=benchmarking_dir,
-		ref_dir=ref_dir,
-		fasta=fasta,
-		docker=BENCHMARKdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size,
-	}
-
-	call benchmark.benchmark as LCL6_2_benchmark {
-		input:
-		vcf=LCL6_2,
-		benchmarking_dir=benchmarking_dir,
-		ref_dir=ref_dir,
-		fasta=fasta,
-		docker=BENCHMARKdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size,
-	}
-
-	call benchmark.benchmark as LCL6_3_benchmark {
-		input:
-		vcf=LCL6_3,
-		benchmarking_dir=benchmarking_dir,
-		ref_dir=ref_dir,
-		fasta=fasta,
-		docker=BENCHMARKdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size,
-	}
-
-	call benchmark.benchmark as LCL7_1_benchmark {
-		input:
-		vcf=LCL7_1,
-		benchmarking_dir=benchmarking_dir,
-		ref_dir=ref_dir,
-		fasta=fasta,
-		docker=BENCHMARKdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size,
-	}	
-
-	call benchmark.benchmark as LCL7_2_benchmark {
-		input:
-		vcf=LCL7_2,
-		benchmarking_dir=benchmarking_dir,
-		ref_dir=ref_dir,
-		fasta=fasta,
-		docker=BENCHMARKdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size,
-	}	
-
-	call benchmark.benchmark as LCL7_3_benchmark {
-		input:
-		vcf=LCL7_3,
-		benchmarking_dir=benchmarking_dir,
-		ref_dir=ref_dir,
-		fasta=fasta,
-		docker=BENCHMARKdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size,
-	}	
-
-
-	call benchmark.benchmark as LCL8_1_benchmark {
-		input:
-		vcf=LCL8_1,
-		benchmarking_dir=benchmarking_dir,
-		ref_dir=ref_dir,
-		fasta=fasta,
-		docker=BENCHMARKdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size,
-	}
-
-	call benchmark.benchmark as LCL8_2_benchmark {
-		input:
-		vcf=LCL8_2,
-		benchmarking_dir=benchmarking_dir,
-		ref_dir=ref_dir,
-		fasta=fasta,
-		docker=BENCHMARKdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size,
-	}
-
-	call benchmark.benchmark as LCL8_3_benchmark {
-		input:
-		vcf=LCL8_3,
-		benchmarking_dir=benchmarking_dir,
-		ref_dir=ref_dir,
-		fasta=fasta,
-		docker=BENCHMARKdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size,
-	}
 
-	call merge_family.merge_family as merge_family_1 {
+	call filter_bed.filter_bed as filter_bed {
 		input:
-		LCL5_vcf_gz=LCL5_1_benchmark.rtg_vcf,
-		LCL5_vcf_idx=LCL5_1_benchmark.rtg_vcf_index,
-		LCL6_vcf_gz=LCL6_1_benchmark.rtg_vcf,
-		LCL6_vcf_idx=LCL6_1_benchmark.rtg_vcf_index,
-		LCL7_vcf_gz=LCL7_1_benchmark.rtg_vcf,
-		LCL7_vcf_idx=LCL7_1_benchmark.rtg_vcf_index,
-		LCL8_vcf_gz=LCL8_1_benchmark.rtg_vcf,
-		LCL8_vcf_idx=LCL8_1_benchmark.rtg_vcf,
-		project=project,
-		rep="1",
-		docker=BENCHMARKdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size,
-	}
-
-	call merge_family.merge_family as merge_family_2 {
-		input:
-		LCL5_vcf_gz=LCL5_2_benchmark.rtg_vcf,
-		LCL5_vcf_idx=LCL5_2_benchmark.rtg_vcf_index,
-		LCL6_vcf_gz=LCL6_2_benchmark.rtg_vcf,
-		LCL6_vcf_idx=LCL6_2_benchmark.rtg_vcf_index,
-		LCL7_vcf_gz=LCL7_2_benchmark.rtg_vcf,
-		LCL7_vcf_idx=LCL7_2_benchmark.rtg_vcf_index,
-		LCL8_vcf_gz=LCL8_2_benchmark.rtg_vcf,
-		LCL8_vcf_idx=LCL8_2_benchmark.rtg_vcf,
-		project=project,
-		rep="2",
-		docker=BENCHMARKdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size,
-	}
-
-	call merge_family.merge_family as merge_family_3 {
-		input:
-		LCL5_vcf_gz=LCL5_3_benchmark.rtg_vcf,
-		LCL5_vcf_idx=LCL5_3_benchmark.rtg_vcf_index,
-		LCL6_vcf_gz=LCL6_3_benchmark.rtg_vcf,
-		LCL6_vcf_idx=LCL6_3_benchmark.rtg_vcf_index,
-		LCL7_vcf_gz=LCL7_3_benchmark.rtg_vcf,
-		LCL7_vcf_idx=LCL7_3_benchmark.rtg_vcf_index,
-		LCL8_vcf_gz=LCL8_3_benchmark.rtg_vcf,
-		LCL8_vcf_idx=LCL8_3_benchmark.rtg_vcf,
-		project=project,
-		rep="3",
-		docker=BENCHMARKdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size,
-	}
-
-	call mendelian.mendelian as mendelian_1 {
-		input:
-		family_vcf=merge_family_1.merged_vcf,
-		ref_dir=ref_dir,
-		fasta=fasta,
-		docker=MENDELIANdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size		
-	}
-
-	call mendelian.mendelian as mendelian_2 {
-		input:
-		family_vcf=merge_family_2.merged_vcf,
-		ref_dir=ref_dir,
-		fasta=fasta,
-		docker=MENDELIANdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size		
-	}
-
-	call mendelian.mendelian as mendelian_3 {
-		input:
-		family_vcf=merge_family_3.merged_vcf,
-		ref_dir=ref_dir,
-		fasta=fasta,
-		docker=MENDELIANdocker,
-		cluster_config=BIGcluster_config,
-		disk_size=disk_size		
-	}
-
-	call merge_mendelian.merge_mendelian as merge_mendelian_1 {
-		input:
-		D5_trio_vcf=mendelian_1.D5_trio_vcf,
-		D6_trio_vcf=mendelian_1.D6_trio_vcf,
-		family_vcf=merge_family_1.merged_vcf,
-		docker=DIYdocker,
+		bed=bed,
+		benchmark_region=benchmark_region,
+		docker=BEDTOOLSdocker,
 		cluster_config=SMALLcluster_config,
 		disk_size=disk_size
 	}
 
-	call merge_mendelian.merge_mendelian as merge_mendelian_2 {
-		input:
-		D5_trio_vcf=mendelian_2.D5_trio_vcf,
-		D6_trio_vcf=mendelian_2.D6_trio_vcf,
-		family_vcf=merge_family_2.merged_vcf,
-		docker=DIYdocker,
-		cluster_config=SMALLcluster_config,
-		disk_size=disk_size
-	}
-
-	call merge_mendelian.merge_mendelian as merge_mendelian_3 {
-		input:
-		D5_trio_vcf=mendelian_3.D5_trio_vcf,
-		D6_trio_vcf=mendelian_3.D6_trio_vcf,
-		family_vcf=merge_family_3.merged_vcf,
-		docker=DIYdocker,
-		cluster_config=SMALLcluster_config,
-		disk_size=disk_size
-	}
-
-	call quartet_mendelian.quartet_mendelian as quartet_mendelian{
-		input:
-		summary_1=merge_mendelian_1.project_mendelian_summary,
-		summary_2=merge_mendelian_2.project_mendelian_summary,
-		summary_3=merge_mendelian_3.project_mendelian_summary,
-		LCL5_hap_1=LCL5_1_benchmark.summary,
-		LCL5_hap_2=LCL5_2_benchmark.summary,
-		LCL5_hap_3=LCL5_3_benchmark.summary,
-		LCL6_hap_1=LCL6_1_benchmark.summary,
-		LCL6_hap_2=LCL6_2_benchmark.summary,
-		LCL6_hap_3=LCL6_3_benchmark.summary,
-		LCL7_hap_1=LCL7_1_benchmark.summary,
-		LCL7_hap_2=LCL7_2_benchmark.summary,
-		LCL7_hap_3=LCL7_3_benchmark.summary,	
-		LCL8_hap_1=LCL8_1_benchmark.summary,
-		LCL8_hap_2=LCL8_2_benchmark.summary,
-		LCL8_hap_3=LCL8_3_benchmark.summary,
+	scatter (sample in inputSamples){
+
+		call benchmark.benchmark as LCL5_benchmark {
+			input:
+			vcf=sample[0],
+			benchmarking_dir=benchmarking_dir,
+			filtered_bed=filter_bed.filtered_bed,
+			ref_dir=ref_dir,
+			fasta=fasta,
+			docker=BENCHMARKdocker,
+			cluster_config=BIGcluster_config,
+			disk_size=disk_size
+		}
+
+		call benchmark.benchmark as LCL6_benchmark {
+			input:
+			vcf=sample[1],
+			benchmarking_dir=benchmarking_dir,
+			filtered_bed=filter_bed.filtered_bed,
+			ref_dir=ref_dir,
+			fasta=fasta,
+			docker=BENCHMARKdocker,
+			cluster_config=BIGcluster_config,
+			disk_size=disk_size
+		}
+
+		call benchmark.benchmark as LCL7_benchmark {
+			input:
+			vcf=sample[2],
+			benchmarking_dir=benchmarking_dir,
+			filtered_bed=filter_bed.filtered_bed,
+			ref_dir=ref_dir,
+			fasta=fasta,
+			docker=BENCHMARKdocker,
+			cluster_config=BIGcluster_config,
+			disk_size=disk_size
+		}
+
+		call benchmark.benchmark as LCL8_benchmark {
+			input:
+			vcf=sample[3],
+			benchmarking_dir=benchmarking_dir,
+			filtered_bed=filter_bed.filtered_bed,
+			ref_dir=ref_dir,
+			fasta=fasta,
+			docker=BENCHMARKdocker,
+			cluster_config=BIGcluster_config,
+			disk_size=disk_size
+		}
+
+		call merge_family.merge_family as merge_family {
+			input:
+			LCL5_vcf_gz=LCL5_benchmark.rtg_vcf,
+			LCL5_vcf_idx=LCL5_benchmark.rtg_vcf_index,
+			LCL6_vcf_gz=LCL6_benchmark.rtg_vcf,
+			LCL6_vcf_idx=LCL6_benchmark.rtg_vcf_index,
+			LCL7_vcf_gz=LCL7_benchmark.rtg_vcf,
+			LCL7_vcf_idx=LCL7_benchmark.rtg_vcf_index,
+			LCL8_vcf_gz=LCL8_benchmark.rtg_vcf,
+			LCL8_vcf_idx=LCL8_benchmark.rtg_vcf,
+			project=project,
+			rep="1",
+			docker=BENCHMARKdocker,
+			cluster_config=BIGcluster_config,
+			disk_size=disk_size,
+		}
+
+		call mendelian.mendelian as mendelian {
+			input:
+			family_vcf=merge_family.merged_vcf,
+			ref_dir=ref_dir,
+			fasta=fasta,
+			docker=MENDELIANdocker,
+			cluster_config=BIGcluster_config,
+			disk_size=disk_size		
+		}
+
+		call merge_mendelian.merge_mendelian as merge_mendelian {
+			input:
+			D5_trio_vcf=mendelian.D5_trio_vcf,
+			D6_trio_vcf=mendelian.D6_trio_vcf,
+			family_vcf=merge_family.merged_vcf,
+			docker=DIYdocker,
+			cluster_config=SMALLcluster_config,
+			disk_size=disk_size
+		}
+
+	}
+
+	call quartet_mendelian.quartet_mendelian as quartet_mendelian {
+		input:
+		summary=merge_mendelian.project_mendelian_summary,
+		LCL5_hap=LCL5_benchmark.summary,
+		LCL6_hap=LCL6_benchmark.summary,
+		LCL7_hap=LCL7_benchmark.summary,
+		LCL8_hap=LCL8_benchmark.summary,
 		docker=DIYdocker,
 		project=project,
 		cluster_config=SMALLcluster_config,