only wgs

tasks/benchmark.wdl

 	File filtered_vcf
 	File benchmarking_dir
 	File ref_dir
-	File? qc_bed
 	String sample = basename(filtered_vcf,".filtered.vcf")
 	String fasta
 	String docker
 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip ${filtered_vcf} -c > ${sample}.rtg.vcf.gz
 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.rtg.vcf.gz
 
-		if [ ${qc_bed} ];then
-			if [[ ${sample} =~ "LCL5" ]];then
-				/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL5.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f ${qc_bed}--threads $nt -o ${sample} -r ${ref_dir}/${fasta}
-		    elif [[ ${sample} =~ "LCL6" ]]; then
-		    	/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL6.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f ${qc_bed} --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
-	        elif [[ ${sample} =~ "LCL7" ]]; then
-	        	/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL7.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f ${qc_bed} --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
-		    elif [[ ${sample} =~ "LCL8" ]]; then
-				/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL8.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f ${qc_bed} --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
-	        else
-	        	echo "only for quartet samples"
-	        fi
+		if [[ ${sample} =~ "LCL5" ]];then
+			/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL5.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+		elif [[ ${sample} =~ "LCL6" ]]; then
+		    /opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL6.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+	    elif [[ ${sample} =~ "LCL7" ]]; then
+	        /opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL7.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+		elif [[ ${sample} =~ "LCL8" ]]; then
+			/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL8.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 	    else
-			if [[ ${sample} =~ "LCL5" ]];then
-				/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL5.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
-		    elif [[ ${sample} =~ "LCL6" ]]; then
-		    	/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL6.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
-	        elif [[ ${sample} =~ "LCL7" ]]; then
-	        	/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL7.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
-		    elif [[ ${sample} =~ "LCL8" ]]; then
-				/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL8.high.confidence.calls.vcf ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
-	        else
-	        	echo "only for quartet samples"	    	
+	        echo "only for quartet samples"
 	    fi
 	>>>
 

tasks/corealigner.wdl

-task corealigner {
-	
-    File ref_dir
-    File dbsnp_dir
-    File dbmills_dir
-
-	String sample
-	String SENTIEON_INSTALL_DIR
-	String docker
-	String cluster_config
-	String fasta
-
-	String dbsnp
-	String db_mills
-	File tumor_recaled_bam
-	File tumor_recaled_bam_index
-	File normal_recaled_bam
-	File normal_recaled_bam_index
-	String disk_size
-
-
-	command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=192.168.0.55:8990
-		nt=$(nproc)
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${tumor_recaled_bam} -i ${normal_recaled_bam} --algo Realigner -k ${db_mills} -k ${dbsnp} ${sample}_corealigned.bam				
-	>>>
-	
-	runtime {
-		docker:docker
-    	cluster: cluster_config
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File corealigner_bam = "${sample}_corealigned.bam"
-		File corealigner_bam_index = "${sample}_corealigned.bam.bai"
-	}	
-}
-
-
-

tasks/deduped_Metrics.wdl

 task deduped_Metrics {
 
     File ref_dir
-    File? bed
 	String SENTIEON_INSTALL_DIR
 	String sample
 	String fasta
 		set -e
 		export SENTIEON_LICENSE=192.168.0.55:8990
 		nt=$(nproc)
-		if [ ${bed} ]; then
-			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} --interval ${bed} --algo CoverageMetrics --omit_base_output ${sample}_deduped_coverage_metrics --algo MeanQualityByCycle ${sample}_deduped_mq_metrics.txt --algo QualDistribution ${sample}_deduped_qd_metrics.txt --algo GCBias --summary ${sample}_deduped_gc_summary.txt ${sample}_deduped_gc_metrics.txt --algo AlignmentStat ${sample}_deduped_aln_metrics.txt --algo InsertSizeMetricAlgo ${sample}_deduped_is_metrics.txt --algo QualityYield ${sample}_deduped_QualityYield.txt --algo WgsMetricsAlgo ${sample}_deduped_WgsMetricsAlgo.txt
-		else
-			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} --algo CoverageMetrics --omit_base_output ${sample}_deduped_coverage_metrics --algo MeanQualityByCycle ${sample}_deduped_mq_metrics.txt --algo QualDistribution ${sample}_deduped_qd_metrics.txt --algo GCBias --summary ${sample}_deduped_gc_summary.txt ${sample}_deduped_gc_metrics.txt --algo AlignmentStat ${sample}_deduped_aln_metrics.txt --algo InsertSizeMetricAlgo ${sample}_deduped_is_metrics.txt --algo QualityYield ${sample}_deduped_QualityYield.txt --algo WgsMetricsAlgo ${sample}_deduped_WgsMetricsAlgo.txt
-		fi
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} --algo CoverageMetrics --omit_base_output ${sample}_deduped_coverage_metrics --algo MeanQualityByCycle ${sample}_deduped_mq_metrics.txt --algo QualDistribution ${sample}_deduped_qd_metrics.txt --algo GCBias --summary ${sample}_deduped_gc_summary.txt ${sample}_deduped_gc_metrics.txt --algo AlignmentStat ${sample}_deduped_aln_metrics.txt --algo InsertSizeMetricAlgo ${sample}_deduped_is_metrics.txt --algo QualityYield ${sample}_deduped_QualityYield.txt --algo WgsMetricsAlgo ${sample}_deduped_WgsMetricsAlgo.txt
 	>>>
 
 	runtime {

tasks/filter_vcf.wdl

+ task filter_vcf {
+	File vcf
+	String project
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+
+		cat ${vcf} | grep '#' > header
+		cat ${vcf} | grep -v '#' > body
+		cat body | grep -w '^chr1\|^chr2\|^chr3\|^chr4\|^chr5\|^chr6\|^chr7\|^chr8\|^chr9\|^chr10\|^chr11\|^chr12\|^chr13\|^chr14\|^chr15\|^chr16\|^chr17\|^chr18\|^chr19\|^chr20\|^chr21\|^chr22\|^chrX' > body.filtered
+		cat header body.filtered > ${project}.filtered.vcf
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File filtered_vcf = "${project}.filtered.vcf"
+	}
+}

tasks/qualimap.wdl

 task qualimap {
 	File bam
 	File bai
-	File? bed
 	String bamname = basename(bam,".bam")
 	String docker
 	String cluster_config
 		set -e
 		nt=$(nproc)
 
-		if [ ${bed} ]; then
-			awk 'BEGIN{OFS="\t"}{sub("\r","",$3);print $1,$2,$3,"",0,"."}' ${bed} > new.bed
-			/opt/qualimap/qualimap bamqc -bam ${bam} -gff new.bed -outformat PDF:HTML -nt $nt -outdir ${bamname} --java-mem-size=60G
-		else
-			/opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir ${bamname} --java-mem-size=60G
-		fi
+		/opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir ${bamname} --java-mem-size=60G
 
 		tar -zcvf ${bamname}_qualimap.zip ${bamname}
 	>>>

workflow.wdl

 import "./tasks/fastqc.wdl" as fastqc
 import "./tasks/fastqscreen.wdl" as fastqscreen
 import "./tasks/merge_family.wdl" as merge_family
-import "./tasks/filter_vcf_bed.wdl" as filter_vcf_bed
+import "./tasks/filter_vcf.wdl" as filter_vcf
 
 
 workflow {{ project_name }} {
 	File? vcf_F7
 	File? vcf_M8
 
-	File? bed
-
 	String SENTIEON_INSTALL_DIR
 	String SENTIEON_LICENSE
 	String SENTIEONdocker
 	File screen_ref_dir
 	File fastq_screen_conf
 	File benchmarking_dir
-	File benchmark_region
 
 	String project
 
 
 		call qualimap.qualimap as qualimap_D5 {
 			input:
-			bed=bed,
 			bam=Dedup_D5.Dedup_bam,
 			bai=Dedup_D5.Dedup_bam_index,
 			docker=QUALIMAPdocker,
 			input:
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			fasta=fasta,
-			bed=bed,
 			ref_dir=ref_dir,
 			Dedup_bam=Dedup_D5.Dedup_bam,
 			Dedup_bam_index=Dedup_D5.Dedup_bam_index,
 			cluster_config=BIGcluster_config
 		}
 
-		call filter_vcf_bed.filter_vcf_bed as filter_vcf_bed_D5 {
+		call filter_vcf.filter_vcf as filter_vcf_D5 {
 			input:
 			vcf=Haplotyper_D5.vcf,
-			bed=bed,
-			benchmark_region=benchmark_region,
 			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
 
 		call benchmark.benchmark as benchmark_D5 {
 			input:
-			filtered_vcf=filter_vcf_bed_D5.filtered_vcf,
+			filtered_vcf=filter_vcf_D5.filtered_vcf,
 			benchmarking_dir=benchmarking_dir,
 			ref_dir=ref_dir,
-			qc_bed=filter_vcf_bed_D5.filtered_bed,
 			fasta=fasta,
 			docker=BENCHMARKdocker,
 			cluster_config=BIGcluster_config,
 
 		call qualimap.qualimap as qualimap_D6 {
 			input:
-			bed=bed,
 			bam=Dedup_D6.Dedup_bam,
 			bai=Dedup_D6.Dedup_bam_index,
 			docker=QUALIMAPdocker,
 			input:
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			fasta=fasta,
-			bed=bed,
 			ref_dir=ref_dir,
 			Dedup_bam=Dedup_D6.Dedup_bam,
 			Dedup_bam_index=Dedup_D6.Dedup_bam_index,
 			cluster_config=BIGcluster_config
 		}
 
-		call filter_vcf_bed.filter_vcf_bed as filter_vcf_bed_D6 {
+		call filter_vcf.filter_vcf as filter_vcf_D6 {
 			input:
 			vcf=Haplotyper_D6.vcf,
-			bed=bed,
-			benchmark_region=benchmark_region,
 			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
 
 		call benchmark.benchmark as benchmark_D6 {
 			input:
-			filtered_vcf=filter_vcf_bed_D6.filtered_vcf,
+			filtered_vcf=filter_vcf_D6.filtered_vcf,
 			benchmarking_dir=benchmarking_dir,
 			ref_dir=ref_dir,
-			qc_bed=filter_vcf_bed_D6.filtered_bed,
 			fasta=fasta,
 			docker=BENCHMARKdocker,
 			cluster_config=BIGcluster_config,
 
 		call qualimap.qualimap as qualimap_F7 {
 			input:
-			bed=bed,
 			bam=Dedup_F7.Dedup_bam,
 			bai=Dedup_F7.Dedup_bam_index,
 			docker=QUALIMAPdocker,
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			fasta=fasta,
 			ref_dir=ref_dir,
-			bed=bed,
 			Dedup_bam=Dedup_F7.Dedup_bam,
 			Dedup_bam_index=Dedup_F7.Dedup_bam_index,
 			sample="F7",
 			cluster_config=BIGcluster_config
 		}
 
-		call filter_vcf_bed.filter_vcf_bed as filter_vcf_bed_F7 {
+		call filter_vcf.filter_vcf as filter_vcf_F7 {
 			input:
 			vcf=Haplotyper_F7.vcf,
-			bed=bed,
-			benchmark_region=benchmark_region,
 			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
 
 		call benchmark.benchmark as benchmark_F7 {
 			input:
-			filtered_vcf=filter_vcf_bed_F7.filtered_vcf,
+			filtered_vcf=filter_vcf_F7.filtered_vcf,
 			benchmarking_dir=benchmarking_dir,
 			ref_dir=ref_dir,
-			qc_bed=filter_vcf_bed_F7.filtered_bed,
 			fasta=fasta,
 			docker=BENCHMARKdocker,
 			cluster_config=BIGcluster_config,
 
 		call qualimap.qualimap as qualimap_M8 {
 			input:
-			bed=bed,
 			bam=Dedup_M8.Dedup_bam,
 			bai=Dedup_M8.Dedup_bam_index,
 			docker=QUALIMAPdocker,
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			fasta=fasta,
 			ref_dir=ref_dir,
-			bed=bed,
 			Dedup_bam=Dedup_M8.Dedup_bam,
 			Dedup_bam_index=Dedup_M8.Dedup_bam_index,
 			sample="M8",
 			cluster_config=BIGcluster_config
 		}
 
-		call filter_vcf_bed.filter_vcf_bed as filter_vcf_bed_M8 {
+		call filter_vcf.filter_vcf as filter_vcf_M8 {
 			input:
 			vcf=Haplotyper_M8.vcf,
-			bed=bed,
-			benchmark_region=benchmark_region,
 			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
 
 		call benchmark.benchmark as benchmark_M8 {
 			input:
-			filtered_vcf=filter_vcf_bed_M8.filtered_vcf,
+			filtered_vcf=filter_vcf_M8.filtered_vcf,
 			benchmarking_dir=benchmarking_dir,
 			ref_dir=ref_dir,
-			qc_bed=filter_vcf_bed_M8.filtered_bed,
 			fasta=fasta,
 			docker=BENCHMARKdocker,
 			cluster_config=BIGcluster_config,
 	}
 
 	if (vcf_D5!= "") {
-		call filter_vcf_bed.filter_vcf_bed as filter_vcf_bed_D5_vcf {
+		call filter_vcf.filter_vcf as filter_vcf_D5_vcf {
 			input:
 			vcf=vcf_D5,
-			bed=bed,
-			benchmark_region=benchmark_region,
 			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
 
 		call benchmark.benchmark as benchmark_D5_vcf {
 			input:
-			filtered_vcf=filter_vcf_bed_D5_vcf.filtered_vcf,
+			filtered_vcf=filter_vcf_D5_vcf.filtered_vcf,
 			benchmarking_dir=benchmarking_dir,
 			ref_dir=ref_dir,
-			qc_bed=filter_vcf_bed_D5.filtered_bed,
 			fasta=fasta,
 			docker=BENCHMARKdocker,
 			cluster_config=BIGcluster_config,
 			disk_size=disk_size
 		}
 
-		call filter_vcf_bed.filter_vcf_bed as filter_vcf_bed_D6_vcf {
+		call filter_vcf.filter_vcf as filter_vcf_D6_vcf {
 			input:
 			vcf=vcf_D6,
-			bed=bed,
-			benchmark_region=benchmark_region,
 			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
 
 		call benchmark.benchmark as benchmark_D6_vcf {
 			input:
-			filtered_vcf=filter_vcf_bed_D6.filtered_vcf,
+			filtered_vcf=filter_vcf_D6_vcf.filtered_vcf,
 			benchmarking_dir=benchmarking_dir,
 			ref_dir=ref_dir,
-			qc_bed=filter_vcf_bed_D6.filtered_bed,
 			fasta=fasta,
 			docker=BENCHMARKdocker,
 			cluster_config=BIGcluster_config,
 			disk_size=disk_size
 		}
 
-		call filter_vcf_bed.filter_vcf_bed as filter_vcf_bed_F7_vcf {
+		call filter_vcf.filter_vcf as filter_vcf_F7_vcf {
 			input:
 			vcf=vcf_F7,
-			bed=bed,
-			benchmark_region=benchmark_region,
 			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
 
 		call benchmark.benchmark as benchmark_F7_vcf {
 			input:
-			filtered_vcf=filter_vcf_bed_F7_vcf.filtered_vcf,
+			filtered_vcf=filter_vcf_F7_vcf.filtered_vcf,
 			benchmarking_dir=benchmarking_dir,
 			ref_dir=ref_dir,
-			qc_bed=filter_vcf_bed_F7.filtered_bed,
 			fasta=fasta,
 			docker=BENCHMARKdocker,
 			cluster_config=BIGcluster_config,
 			disk_size=disk_size
 		}
 
-		call filter_vcf_bed.filter_vcf_bed as filter_vcf_bed_M8_vcf {
+		call filter_vcf.filter_vcf as filter_vcf_M8_vcf {
 			input:
 			vcf=vcf_M8,
-			bed=bed,
-			benchmark_region=benchmark_region,
 			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
 
 		call benchmark.benchmark as benchmark_M8_vcf {
 			input:
-			filtered_vcf=filter_vcf_bed_M8_vcf.filtered_vcf,
+			filtered_vcf=filter_vcf_M8_vcf.filtered_vcf,
 			benchmarking_dir=benchmarking_dir,
 			ref_dir=ref_dir,
-			qc_bed=filter_vcf_bed_M8.filtered_bed,
 			fasta=fasta,
 			docker=BENCHMARKdocker,
 			cluster_config=BIGcluster_config,