first commit

fastq_screen.conf

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+# This is an example configuration file for FastQ Screen
+
+############################
+## Bowtie, Bowtie 2 or BWA #
+############################
+## If the Bowtie, Bowtie 2 or BWA binary is not in your PATH, you can set 
+## this value to tell the program where to find your chosen aligner.  Uncomment 
+## the relevant line below and set the appropriate location.  Please note, 
+## this path should INCLUDE the executable filename.
+
+#BOWTIE	/usr/local/bin/bowtie/bowtie
+#BOWTIE2 /usr/local/bowtie2/bowtie2
+#BWA /usr/local/bwa/bwa
+
+
+
+############################################
+## Bismark (for bisulfite sequencing only) #
+############################################
+## If the Bismark binary is not in your PATH then you can set this value to 
+## tell the program where to find it.  Uncomment the line below and set the 
+## appropriate location. Please note, this path should INCLUDE the executable 
+## filename.
+
+#BISMARK	/usr/local/bin/bismark/bismark
+
+
+
+############
+## Threads #
+############
+## Genome aligners can be made to run across multiple CPU cores to speed up 
+## searches.  Set this value to the number of cores you want for mapping reads.
+
+THREADS		32
+
+
+
+##############
+## DATABASES #
+##############
+## This section enables you to configure multiple genomes databases (aligner index 
+## files) to search against in your screen.  For each genome you need to provide a 
+## database name (which can't contain spaces) and the location of the aligner index 
+## files.
+##
+## The path to the index files SHOULD INCLUDE THE BASENAME of the index, e.g:
+## /data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37
+## Thus, the index files (Homo_sapiens.GRCh37.1.bt2, Homo_sapiens.GRCh37.2.bt2, etc.) 
+## are found in a folder named 'GRCh37'.
+##
+## If, for example, the Bowtie, Bowtie2 and BWA indices of a given genome reside in 
+## the SAME FOLDER, a SINLGE path may be provided to ALL the of indices.  The index 
+## used will be the one compatible with the chosen aligner (as specified using the 
+## --aligner flag).  
+##
+## The entries shown below are only suggested examples, you can add as many DATABASE 
+## sections as required, and you can comment out or remove as many of the existing 
+## entries as desired.  We suggest including genomes and sequences that may be sources 
+## of contamination either because they where run on your sequencer previously, or may 
+## have contaminated your sample during the library preparation step.
+##
+## Human - sequences available from
+## ftp://ftp.ensembl.org/pub/current/fasta/homo_sapiens/dna/
+#DATABASE	Human	/data/public/Genomes/Human_Bowtie/GRCh37/Homo_sapiens.GRCh37
+##
+## Mouse - sequence available from
+## ftp://ftp.ensembl.org/pub/current/fasta/mus_musculus/dna/
+#DATABASE	Mouse	/data/public/Genomes/Mouse/NCBIM37/Mus_musculus.NCBIM37
+##
+## Ecoli- sequence available from EMBL accession U00096.2
+#DATABASE	Ecoli	/data/public/Genomes/Ecoli/Ecoli
+##
+## PhiX - sequence available from Refseq accession NC_001422.1
+#DATABASE	PhiX	/data/public/Genomes/PhiX/phi_plus_SNPs
+##
+## Adapters - sequence derived from the FastQC contaminats file found at: www.bioinformatics.babraham.ac.uk/projects/fastqc
+#DATABASE	Adapters	/data/public/Genomes/Contaminants/Contaminants
+##
+## Vector - Sequence taken from the UniVec database
+## http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html
+#DATABASE	Vectors		/data/public/Genomes/Vectors/Vectors
+
+DATABASE	Human	/cromwell_root/tmp/fastq_screen_reference/genome
+DATABASE	Mouse	/cromwell_root/tmp/fastq_screen_reference/mouse
+DATABASE	ERCC	/cromwell_root/tmp/fastq_screen_reference/ERCC
+DATABASE	EColi	/cromwell_root/tmp/fastq_screen_reference/ecoli
+DATABASE	Adapter	/cromwell_root/tmp/fastq_screen_reference/adapters
+DATABASE	Vector	/cromwell_root/tmp/fastq_screen_reference/vector
+DATABASE	rRNA	/cromwell_root/tmp/fastq_screen_reference/rRNARef
+DATABASE	Virus	/cromwell_root/tmp/fastq_screen_reference/viral
+DATABASE	Yeast	/cromwell_root/tmp/fastq_screen_reference/GCF_000146045.2_R64_genomic_modify
+DATABASE	Mitoch	/cromwell_root/tmp/fastq_screen_reference/Human_mitoch
+DATABASE	Phix	/cromwell_root/tmp/fastq_screen_reference/phix

inputSamplesFileExamples.tsv

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+#read1	#read2	#bam	#bai	#vcf	#sample_mark	#sample_name	#_aln.metrics.txt	#_dedup_metrics.txt	#_is_metrics.txt	#_deduped_coverage_metrics.sample_summary
+oss://chinese-quartet/quartet-test-data/fastqfiles/Fudan_DNA_LCL5_R1.fastq.gz	oss://chinese-quartet/quartet-test-data/fastqfiles/Fudan_DNA_LCL5_R2.fastq.gz	oss://choppy-cromwell-result/test-choppy/wgs_quartettest_renluyao_0827/7a72d0e6-302d-43ca-b6b0-daeaa0236d06/call-Dedup/Fudan_DNA_LCL5.sorted.deduped.bam	oss://choppy-cromwell-result/test-choppy/wgs_quartettest_renluyao_0827/7a72d0e6-302d-43ca-b6b0-daeaa0236d06/call-Dedup/Fudan_DNA_LCL5.sorted.deduped.bam.bai	oss://choppy-cromwell-result/test-choppy/wgs_quartettest_renluyao_0827/7a72d0e6-302d-43ca-b6b0-daeaa0236d06/call-Haplotyper/Fudan_DNA_LCL5_hc.vcf	LCL5
+oss://chinese-quartet/quartet-test-data/fastqfiles/Fudan_DNA_LCL6_R1.fastq.gz	oss://chinese-quartet/quartet-test-data/fastqfiles/Fudan_DNA_LCL6_R2.fastq.gz	oss://choppy-cromwell-result/test-choppy/wgs_quartettest_renluyao_0827/e85d0acb-f750-48b7-87e6-f28766dd16b9/call-Dedup/Fudan_DNA_LCL6.sorted.deduped.bam	oss://choppy-cromwell-result/test-choppy/wgs_quartettest_renluyao_0827/e85d0acb-f750-48b7-87e6-f28766dd16b9/call-Dedup/Fudan_DNA_LCL6.sorted.deduped.bam.bai	oss://choppy-cromwell-result/test-choppy/wgs_quartettest_renluyao_0827/e85d0acb-f750-48b7-87e6-f28766dd16b9/call-Haplotyper/Fudan_DNA_LCL6_hc.vcf	LCL6

inputs

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+{
+  "{{ 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 }}.fasta": "GRCh38.d1.vd1.fa",
+  "{{ project_name }}.fastqc.disk_size": "150",
+  "{{ project_name }}.benchmark.cluster_config": "OnDemand ecs.sn1ne.4xlarge img-ubuntu-vpc",
+  "{{ project_name }}.mergeJI.disk_size": "100",
+  "{{ project_name }}.fastqscreen.cluster_config": "OnDemand ecs.sn1ne.4xlarge img-ubuntu-vpc",
+  "{{ project_name }}.fastqc.cluster_config": "OnDemand ecs.sn1ne.4xlarge img-ubuntu-vpc",
+  "{{ project_name }}.inputJIpiarsFile": "{{ inputJIpiarsFile }}",
+  "{{ project_name }}.benchmark.disk_size": "150",
+  "{{ project_name }}.vcfstat.disk_size": "100",
+  "{{ project_name }}.fastqc.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5",
+  "{{ project_name }}.mergeJI.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-tools:latest",
+  "{{ project_name }}.benchmark.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
+  "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
+  "{{ project_name }}.mergeJI.cluster_config": "OnDemand ecs.sn1ne.xlarge img-ubuntu-vpc",
+  "{{ project_name }}.fastqscreen.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",
+  "{{ project_name }}.mergeNum.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/gatk:v2019.01",
+  "{{ project_name }}.JI.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
+  "{{ project_name }}.screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",
+  "{{ project_name }}.mergeNum.disk_size": "100",
+  "{{ project_name }}.JI.disk_size": "100",
+  "{{ project_name }}.fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",
+  "{{ project_name }}.multiqc.cluster_config": "OnDemand ecs.sn1ne.4xlarge img-ubuntu-vpc",
+  "{{ project_name }}.sdf": "oss://chinese-quartet/quartet-storage-data/reference_data/GRCh38.d1.vd1.sdf/",
+  "{{ project_name }}.multiqc.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/multiqc:v1.8",
+  "{{ project_name }}.mergeNum.cluster_config": "OnDemand ecs.sn1ne.xlarge img-ubuntu-vpc",
+  "{{ project_name }}.bamqc.cluster_config": "OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc",
+  "{{ project_name }}.vcfstat.cluster_config": "OnDemand ecs.sn1ne.4xlarge img-ubuntu-vpc",
+  "{{ project_name }}.JI.cluster_config": "OnDemand ecs.sn1ne.4xlarge img-ubuntu-vpc",
+  "{{ project_name }}.fastqscreen.disk_size": "100",
+  "{{ project_name }}.bamqc.disk_size": "500",
+  "{{ project_name }}.multiqc.disk_size": "100",
+  "{{ project_name }}.bamqc.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
+  "{{ project_name }}.ref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/"
+}
+
+{
+  "project_name.benchmarking_dir": "File",
+  "project_name.vcfstat.docker": "String",
+  "project_name.qualimap.docker": "String",
+  "project_name.qualimap.cluster_config": "String",
+  "project_name.fasta": "String",
+  "project_name.fastqc.disk_size": "String",
+  "project_name.mergeSentieon.docker": "String",
+  "project_name.benchmark.cluster_config": "String",
+  "project_name.sentieon.docker": "String",
+  "project_name.fastqscreen.cluster_config": "String",
+  "project_name.fastqc.cluster_config": "String",
+  "project_name.benchmark.disk_size": "String",
+  "project_name.vcfstat.disk_size": "String",
+  "project_name.fastqc.docker": "String",
+  "project_name.sentieon.cluster_config": "String",
+  "project_name.benchmark.docker": "String",
+  "project_name.inputSamplesFile": "File",
+  "project_name.fastqscreen.docker": "String",
+  "project_name.mergeNum.docker": "String",
+  "project_name.screen_ref_dir": "File",
+  "project_name.mergeNum.disk_size": "String",
+  "project_name.fastq_screen_conf": "File",
+  "project_name.multiqc.cluster_config": "String",
+  "project_name.qualimap.disk_size": "String",
+  "project_name.sdf": "File",
+  "project_name.multiqc.docker": "String",
+  "project_name.mergeNum.cluster_config": "String",
+  "project_name.mergeSentieon.disk_size": "String",
+  "project_name.sentieon.disk_size": "String",
+  "project_name.vcfstat.cluster_config": "String",
+  "project_name.mergeSentieon.cluster_config": "String",
+  "project_name.fastqscreen.disk_size": "String",
+  "project_name.multiqc.disk_size": "String",
+  "project_name.ref_dir": "File"
+}

tasks/benchmark.wdl

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+task benchmark {
+	File vcf
+	File benchmarking_dir
+	File ref_dir
+	String sample = basename(vcf,".vcf")
+	String sample_mark
+	String fasta
+	String docker
+	String cluster_config
+	String disk_size
+
+
+	command <<<
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		mkdir -p /cromwell_root/tmp
+		cp -r ${ref_dir} /cromwell_root/tmp/
+
+		export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa
+
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip ${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 [ ${sample_mark} == "LCL5" ];then
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.vcf.gz ${sample}.rtg.vcf.gz --threads $nt -o ${sample}
+	    elif [ ${sample_mark} == "LCL6" ]; then
+	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.vcf.gz ${sample}.rtg.vcf.gz --threads $nt -o ${sample}
+        elif [ ${sample_mark} == "LCL7" ]; then
+        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.vcf.gz ${sample}.rtg.vcf.gz --threads $nt -o ${sample}
+	    elif [ ${sample_mark} == "LCL8" ]; then
+			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.vcf.gz ${sample}.rtg.vcf.gz --threads $nt -o ${sample}
+        else
+        	echo "only for quartet samples"
+        fi		
+	>>>
+
+	runtime {
+		docker:docker
+		cluster:cluster_config
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File rtg_vcf = "${sample}.rtg.vcf.gz"
+		File rtg_vcf_index = "${sample}.rtg.vcf.gz.tbi"
+		File gzip_vcf = "${sample}.vcf.gz"
+		File gzip_vcf_index = "${sample}.vcf.gz.tbi"
+		File roc_all_csv = "${sample}.roc.all.csv.gz"
+		File roc_indel = "${sample}.roc.Locations.INDEL.csv.gz"
+		File roc_indel_pass = "${sample}.roc.Locations.INDEL.PASS.csv.gz"
+		File roc_snp = "${sample}.roc.Locations.SNP.csv.gz"
+		File roc_snp_pass = "${sample}.roc.Locations.SNP.PASS.csv.gz"
+		File summary = "${sample}.summary.csv"
+		File extended = "${sample}.extended.csv"
+		File metrics = "${sample}.metrics.json.gz"
+	}
+}

tasks/fastqc.wdl

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+task fastqc {
+	File read1
+	File read2
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		fastqc -t $nt -o ./ ${read1}
+		fastqc -t $nt -o ./ ${read2}
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File read1_html = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_fastqc.html")
+		File read1_zip = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_fastqc.zip")
+		File read2_html = sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_fastqc.html")
+		File read2_zip = sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_fastqc.zip")
+	}
+}

tasks/fastqscreen.wdl

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+task fastq_screen {
+	File read1
+	File read2
+	File screen_ref_dir
+	File fastq_screen_conf
+	String read1name = basename(read1,".fastq.gz")
+	String read2name = basename(read2,".fastq.gz")
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		mkdir -p /cromwell_root/tmp
+		cp -r ${screen_ref_dir} /cromwell_root/tmp/
+		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read1}
+		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read2}
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File png1 = "${read1name}_screen.png"
+		File txt1 = "${read1name}_screen.txt"
+		File html1 = "${read1name}_screen.html"
+		File png2 = "${read2name}_screen.png"
+		File txt2 = "${read2name}_screen.txt"
+		File html2 = "${read2name}_screen.html"
+	}
+}

tasks/mergeNum.wdl

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+task mergeNum {
+	Array[File] vcfnumber
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		for i in ${sep=" " vcfnumber}
+		do
+		  cat $i | cut -d':' -f2 | tr '\n' '\t' | sed s'/\t$/\n/g' >> vcfstats
+		done
+		sed '1i\File\tFailed Filters\tPassed Filters\tSNPs\tMNPs\tInsertions\tDeletions\tIndels\tSame as reference\tSNP Transitions/Transversions\tTotal Het/Hom ratio\tSNP Het/Hom ratio\tMNP Het/Hom ratio\tInsertion Het/Hom ratio\tDeletion Het/Hom ratio\tIndel Het/Hom ratio\tInsertion/Deletion ratio\tIndel/SNP+MNP ratio' vcfstats > vcfstats.txt
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk:"cloud_ssd 40"
+    	dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File vcfstat="vcfstats.txt"
+	}
+}

tasks/mergeSentieon.wdl

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+task mergeSentieon {
+	Array[File] aln_metrics_header
+	Array[File] aln_metrics_data
+
+	Array[File] dedup_metrics_header
+	Array[File] dedup_metrics_data
+
+	Array[File] is_metrics_header
+	Array[File] is_metrics_data
+
+	Array[File] deduped_coverage_header
+	Array[File] deduped_coverage_data
+
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		cat ${aln_metrics_header} | sed -n '1,1p' | cat - ${aln_metrics_data} > aln_metrics.txt
+		cat ${dedup_metrics_header} | sed -n '1,1p' | cat - ${dedup_metrics_data} > dedup_metrics.txt
+		cat ${is_metrics_header} | sed -n '1,1p' | cat - ${is_metrics_data} > is_metrics.txt
+		cat ${deduped_coverage_header} | sed -n '1,1p' | cat - ${deduped_coverage_data} > deduped_coverage.txt
+	>>>
+
+	runtime {
+		docker:docker
+		cluster:cluster_config
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File aln_metrics_merge = "aln_metrics.txt"
+		File dedup_metrics_merge = "dedup_metrics.txt"
+		File is_metrics_merge = "is_metrics.txt"
+		File deduped_coverage_merge = "deduped_coverage.txt"
+	}
+}

tasks/multiqc.wdl

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+task multiqc {
+
+	Array[File] read1_zip
+	Array[File] read2_zip
+
+	Array[File] txt1
+	Array[File] txt2
+
+	Array[File] zip
+
+	Array[File] summary
+
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		mkdir -p /cromwell_root/tmp/fastqc
+		mkdir -p /cromwell_root/tmp/fastqscreen
+		mkdir -p /cromwell_root/tmp/bamqc
+		mkdir -p /cromwell_root/tmp/benchmark
+
+		cp ${sep=" " read1_zip} ${sep=" " read2_zip} /cromwell_root/tmp/fastqc
+		cp ${sep=" " txt1} ${sep=" " txt2} /cromwell_root/tmp/fastqscreen
+		cp ${sep=" " summary} /cromwell_root/tmp/benchmark
+		for i in ${sep=" " zip}
+		do
+		  tar -zxvf $i -C /cromwell_root/tmp/bamqc
+		done
+
+		multiqc /cromwell_root/tmp/
+	
+	>>>
+
+	runtime {
+		docker:docker
+		cluster:cluster_config
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File multiqc_html = "multiqc_report.html"
+		Array[File] multiqc_txt = glob("multiqc_data/*")
+	}
+}

tasks/qualimap.wdl

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+task qualimap {
+	File bam
+	File bai
+	String bamname = basename(bam,".bam")
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		/opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir ${bamname} --java-mem-size=32G 
+		tar -zcvf ${bamname}_qualimap.zip ${bamname}
+	>>>
+
+	runtime {
+		docker:docker
+		cluster:cluster_config
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File zip = "${bamname}_qualimap.zip"
+	}
+}

tasks/sentieon.wdl

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+task sentieon {
+	File aln_metrics
+	File dedup_metrics
+	File is_metrics
+	File deduped_coverage
+	String sample_name
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		cat ${aln_metrics} | sed -n '2,2p'  > aln_metrics.header
+		cat ${aln_metrics} | sed -n '2,2p'  > ${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
+		cat ${is_metrics} | sed -n '3,3p' > ${sample_name}.is_metrics
+		cat ${deduped_coverage} | sed -n '1,1p' > deduped_coverage.header
+		cat ${deduped_coverage} | sed -n '2,2p' > ${sample_name}.deduped_coverage
+	>>>
+
+	runtime {
+		docker:docker
+		cluster:cluster_config
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File aln_metrics_header = "aln_metrics.header"
+		File aln_metrics_data = "${sample_name}.aln_metrics"
+		File dedup_metrics_header = "dedup_metrics.header"
+		File dedup_metrics_data = "${sample_name}.dedup_metrics"
+		File is_metrics_header = "is_metrics.header"
+		File is_metrics_data = "${sample_name}.is_metrics"
+		File deduped_coverage_header = "deduped_coverage.header"
+		File deduped_coverage_data = "${sample_name}.deduped_coverage"
+	}
+}

tasks/vcfstat.wdl

@@ -0,0 +1,25 @@
+task vcfstat {
+	File rtg_vcf
+	File rtg_vcf_index
+	String sample_name
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfstats ${rtg_vcf} > ${sample_name}.stats.txt
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk:"cloud_ssd 40"
+    	dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File vcfnumber="${sample_name}.stats.txt"
+	}
+}

workflow.wdl

@@ -0,0 +1,97 @@
+import "./tasks/fastqc.wdl" as fastqc
+import "./tasks/fastqscreen.wdl" as fastqscreen
+import "./tasks/qualimap.wdl" as qualimap
+import "./tasks/benchmark.wdl" as benchmark
+import "./tasks/vcfstat.wdl" as vcfstat
+import "./tasks/sentieon.wdl" as sentieon
+import "./tasks/multiqc.wdl" as multiqc
+import "./tasks/mergeNum.wdl" as mergeNum
+import "./tasks/mergeSentieon.wdl" as mergeSentieon
+
+
+workflow project_name {
+
+	File inputSamplesFile
+	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
+	File screen_ref_dir
+	File fastq_screen_conf
+	File benchmarking_dir
+	File ref_dir
+	String fasta
+	File sdf
+
+	scatter (sample in inputSamples) {
+		call fastqc.fastqc as fastqc {
+			input:
+			read1=sample[0],
+			read2=sample[1]
+		}
+
+		call fastqscreen.fastq_screen as fastqscreen {
+			input:
+			read1=sample[0],
+			read2=sample[1],
+			screen_ref_dir=screen_ref_dir,
+			fastq_screen_conf=fastq_screen_conf
+		}
+
+		call qualimap.qualimap as qualimap {
+			input:
+			bam=sample[2],
+			bai=sample[3]
+		}
+
+		call benchmark.benchmark as benchmark {
+			input:
+			vcf=sample[4],
+			benchmarking_dir=benchmarking_dir,
+			ref_dir=ref_dir,
+			sample_mark=sample[5],
+			fasta=fasta
+		}
+
+		call vcfstat.vcfstat as vcfstat {
+			input:
+			rtg_vcf=benchmark.rtg_vcf,
+			rtg_vcf_index=benchmark.rtg_vcf_index,
+			sample_name=sample[6]
+		}
+
+		call sentieon.sentieon as sentieon {
+			input:
+			aln_metrics=sample[7],
+			dedup_metrics=sample[8],
+			is_metrics=sample[9],
+			deduped_coverage=sample[10],
+			sample_name=sample[6]
+		}
+
+	}
+	call multiqc.multiqc as multiqc {
+		input:
+		read1_zip=fastqc.read1_zip,
+		read2_zip=fastqc.read2_zip,
+		txt1=fastqscreen.txt1,
+		txt2=fastqscreen.txt2,
+		zip=qualimap.zip,
+		summary=benchmark.summary
+	}
+
+	call mergeNum.mergeNum as mergeNum {
+		input:
+		vcfnumber=vcfstat.vcfnumber
+	}
+
+	call mergeSentieon.mergeSentieon as mergeSentieon {
+		input:
+		aln_metrics_header=sentieon.aln_metrics_header,
+		aln_metrics_data=sentieon.aln_metrics_data,
+		dedup_metrics_header=sentieon.dedup_metrics_header,
+		dedup_metrics_data=sentieon.dedup_metrics_data,
+		is_metrics_header=sentieon.is_metrics_header,
+		is_metrics_data=sentieon.is_metrics_data,
+		deduped_coverage_header=sentieon.deduped_coverage_header,
+		deduped_coverage_data=sentieon.deduped_coverage_data
+	}
+}
+