first commit

inputs

@@ -0,0 +1,10 @@
+{
+  "{{ project_name }}.SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
+  "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
+  "{{ project_name }}.disk_size": "500",
+  "{{ project_name }}.gvcf_dir": "{{ gvcf_dir }}",
+  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
+  "{{ project_name }}.project": "{{ project }}",
+  "{{ project_name }}.cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
+  "{{ project_name }}.ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"
+}

tasks/BQSR.wdl

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+task BQSR {
+	
+    File ref_dir
+    File dbsnp_dir
+    File dbmills_dir
+	String sample
+	String SENTIEON_INSTALL_DIR
+	String fasta
+	String dbsnp
+	String db_mills
+	File realigned_bam
+	File realigned_bam_index
+	String docker
+	String cluster_config
+	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 ${realigned_bam} --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table
+
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${realigned_bam} -q ${sample}_recal_data.table --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table.post --algo ReadWriter ${sample}.sorted.deduped.realigned.recaled.bam
+
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --algo QualCal --plot --before ${sample}_recal_data.table --after ${sample}_recal_data.table.post ${sample}_recal_data.csv
+
+		${SENTIEON_INSTALL_DIR}/bin/sentieon plot QualCal -o ${sample}_bqsrreport.pdf ${sample}_recal_data.csv
+
+	>>>
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"	
+	}
+
+	output {
+		File recal_table = "${sample}_recal_data.table"
+		File recal_post = "${sample}_recal_data.table.post"
+		File recaled_bam = "${sample}.sorted.deduped.realigned.recaled.bam"
+		File recaled_bam_index = "${sample}.sorted.deduped.realigned.recaled.bam.bai"
+		File recal_csv = "${sample}_recal_data.csv"
+		File bqsrreport_pdf = "${sample}_bqsrreport.pdf"
+	}
+}

tasks/Dedup.wdl

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+task Dedup {
+
+	String SENTIEON_INSTALL_DIR
+	String sample
+
+	File sorted_bam
+	File sorted_bam_index
+	String docker
+	String cluster_config
+	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 -t $nt -i ${sorted_bam} --algo LocusCollector --fun score_info ${sample}_score.txt
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sorted_bam} --algo Dedup --rmdup --score_info ${sample}_score.txt --metrics ${sample}_dedup_metrics.txt ${sample}.sorted.deduped.bam	
+	>>>
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File score = "${sample}_score.txt"
+		File dedup_metrics = "${sample}_dedup_metrics.txt"
+		File Dedup_bam = "${sample}.sorted.deduped.bam"
+		File Dedup_bam_index = "${sample}.sorted.deduped.bam.bai"
+	}
+}
+
+
+
+
+
+

tasks/GVCFtyper_chr3.wdl

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+task GVCFtyper_chr3 {
+	
+    File ref_dir
+	String SENTIEON_INSTALL_DIR
+	String fasta
+	String gvcf_dir
+	String project
+	String docker
+	String cluster_config
+	String disk_size
+
+command <<<
+		set -o pipefail
+		set -e
+		export SENTIEON_LICENSE=192.168.0.55:8990
+		nt=$(nproc)
+		mkdir -p /cromwell_root/tmp
+		cp -r ${gvcf_dir} /cromwell_root/tmp/
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo GVCFtyper ${project}.joint.g.vcf /cromwell_root/tmp/*.chr3.vcf
+	>>>
+	
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File gvcf = "${project}.chr3.joint.g.vcf"
+		File gvcf_idx = "${project}.chr3.joint.g.vcf.idx"
+	}
+}
+
+

tasks/GVCFtyper_chr4.wdl

@@ -0,0 +1,33 @@
+task GVCFtyper_chr4 {
+	
+    File ref_dir
+	String SENTIEON_INSTALL_DIR
+	String fasta
+	String gvcf_dir
+	String project
+	String docker
+	String cluster_config
+	String disk_size
+
+command <<<
+		set -o pipefail
+		set -e
+		export SENTIEON_LICENSE=192.168.0.55:8990
+		nt=$(nproc)
+		mkdir -p /cromwell_root/tmp
+		cp -r ${gvcf_dir} /cromwell_root/tmp/
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo GVCFtyper ${project}.joint.g.vcf /cromwell_root/tmp/*.chr4.vcf
+	>>>
+	
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File gvcf = "${project}.chr4.joint.g.vcf"
+		File gvcf_idx = "${project}.chr4.joint.g.vcf.idx"
+	}
+}

tasks/GVCFtyper_chr7.wdl

@@ -0,0 +1,33 @@
+task GVCFtyper_chr7 {
+	
+    File ref_dir
+	String SENTIEON_INSTALL_DIR
+	String fasta
+	String gvcf_dir
+	String project
+	String docker
+	String cluster_config
+	String disk_size
+
+command <<<
+		set -o pipefail
+		set -e
+		export SENTIEON_LICENSE=192.168.0.55:8990
+		nt=$(nproc)
+		mkdir -p /cromwell_root/tmp
+		cp -r ${gvcf_dir} /cromwell_root/tmp/
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo GVCFtyper ${project}.joint.g.vcf /cromwell_root/tmp/*.chr7.vcf
+	>>>
+	
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File gvcf = "${project}.chr7.joint.g.vcf"
+		File gvcf_idx = "${project}.chr7.joint.g.vcf.idx"
+	}
+}

tasks/GVCFtyper_chr8.wdl

@@ -0,0 +1,33 @@
+task GVCFtyper_chr8 {
+	
+    File ref_dir
+	String SENTIEON_INSTALL_DIR
+	String fasta
+	String gvcf_dir
+	String project
+	String docker
+	String cluster_config
+	String disk_size
+
+command <<<
+		set -o pipefail
+		set -e
+		export SENTIEON_LICENSE=192.168.0.55:8990
+		nt=$(nproc)
+		mkdir -p /cromwell_root/tmp
+		cp -r ${gvcf_dir} /cromwell_root/tmp/
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo GVCFtyper ${project}.joint.g.vcf /cromwell_root/tmp/*.chr8.vcf
+	>>>
+	
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File gvcf = "${project}.chr8.joint.g.vcf"
+		File gvcf_idx = "${project}.chr8.joint.g.vcf.idx"
+	}
+}

tasks/GVCFtyper_chrX.wdl

@@ -0,0 +1,33 @@
+task GVCFtyper_chrX {
+	
+    File ref_dir
+	String SENTIEON_INSTALL_DIR
+	String fasta
+	String gvcf_dir
+	String project
+	String docker
+	String cluster_config
+	String disk_size
+
+command <<<
+		set -o pipefail
+		set -e
+		export SENTIEON_LICENSE=192.168.0.55:8990
+		nt=$(nproc)
+		mkdir -p /cromwell_root/tmp
+		cp -r ${gvcf_dir} /cromwell_root/tmp/
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo GVCFtyper ${project}.joint.g.vcf /cromwell_root/tmp/*.chrX.vcf
+	>>>
+	
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File gvcf = "${project}.chrX.joint.g.vcf"
+		File gvcf_idx = "${project}.chrX.joint.g.vcf.idx"
+	}
+}

tasks/Haplotyper.wdl

@@ -0,0 +1,35 @@
+task Haplotyper {
+	
+	
+    File ref_dir
+	String SENTIEON_INSTALL_DIR
+	String fasta
+	File recaled_bam
+	File recaled_bam_index
+	String sample
+	String docker
+	String cluster_config
+	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 ${recaled_bam} --algo Haplotyper --emit_mode gvcf ${sample}_hc.g.vcf
+	>>>
+	
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File vcf = "${sample}_hc.g.vcf"
+		File vcf_idx = "${sample}_hc.g.vcf.idx"
+	}
+}
+
+

tasks/Metrics.wdl

@@ -0,0 +1,56 @@
+task Metrics {
+
+
+    File ref_dir
+	String SENTIEON_INSTALL_DIR
+	String sample
+	String docker
+	String cluster_config
+
+	String fasta
+	File sorted_bam
+	File sorted_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 ${sorted_bam} --algo MeanQualityByCycle ${sample}_mq_metrics.txt --algo QualDistribution ${sample}_qd_metrics.txt --algo GCBias --summary ${sample}_gc_summary.txt ${sample}_gc_metrics.txt --algo AlignmentStat ${sample}_aln_metrics.txt --algo InsertSizeMetricAlgo ${sample}_is_metrics.txt --algo CoverageMetrics --omit_base_output ${sample}_coverage_metrics
+
+		${SENTIEON_INSTALL_DIR}/bin/sentieon plot metrics -o ${sample}_metrics_report.pdf gc=${sample}_gc_metrics.txt qd=${sample}_qd_metrics.txt mq=${sample}_mq_metrics.txt isize=${sample}_is_metrics.txt
+	>>>
+	
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File qd_metrics = "${sample}_qd_metrics.txt"
+		File qd_metrics_pdf = "${sample}_qd_metrics.pdf"
+		File mq_metrics = "${sample}_mq_metrics.txt"
+		File mq_metrics_pdf = "${sample}_mq_metrics.pdf"
+		File is_metrics = "${sample}_is_metrics.txt"
+		File is_metrics_pdf = "${sample}_is_metrics.pdf"
+		File gc_summary = "${sample}_gc_summary.txt"
+		File gc_metrics = "${sample}_gc_metrics.txt"
+		File gc_metrics_pdf = "${sample}_gc_metrics.pdf"
+		File aln_metrics = "${sample}_aln_metrics.txt"
+		File coverage_metrics_sample_summary = "${sample}_coverage_metrics.sample_summary"
+		File coverage_metrics_sample_statistics = "${sample}_coverage_metrics.sample_statistics"
+		File coverage_metrics_sample_interval_statistics = "${sample}_coverage_metrics.sample_interval_statistics"
+		File coverage_metrics_sample_cumulative_coverage_proportions = "${sample}_coverage_metrics.sample_cumulative_coverage_proportions"
+		File coverage_metrics_sample_cumulative_coverage_counts = "${sample}_coverage_metrics.sample_cumulative_coverage_counts"
+	}
+
+}
+
+
+
+
+

tasks/Realigner.wdl

@@ -0,0 +1,41 @@
+task Realigner {
+
+    File ref_dir
+    File dbmills_dir
+
+	String SENTIEON_INSTALL_DIR
+	String sample
+	String fasta
+
+	File Dedup_bam
+	File Dedup_bam_index
+	String db_mills
+	String docker	
+	String cluster_config
+	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 ${Dedup_bam} --algo Realigner -k ${dbmills_dir}/${db_mills} ${sample}.sorted.deduped.realigned.bam
+	
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File realigner_bam = "${sample}.sorted.deduped.realigned.bam"
+		File realigner_bam_index = "${sample}.sorted.deduped.realigned.bam.bai"
+
+	}
+}
+
+

tasks/TNscope.wdl

@@ -0,0 +1,42 @@
+task TNscope {
+
+	File ref_dir
+    File dbsnp_dir
+    
+
+	String SENTIEON_INSTALL_DIR
+	String tumor_name
+	String normal_name
+	String docker
+	String cluster_config
+
+	String fasta
+	File corealigner_bam
+	File corealigner_bam_index
+	String dbsnp
+	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 ${corealigner_bam} --algo TNscope --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}.TNscope.TN.vcf
+		
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File TNscope_vcf= "${sample}.TNscope.TN.vcf"
+		File TNscope_vcf_index = "${sample}.TNscope.TN.vcf.idx"
+	}
+
+}

tasks/TNseq.wdl

@@ -0,0 +1,43 @@
+task TNseq {
+	
+    File ref_dir
+    File dbsnp_dir
+
+	String SENTIEON_INSTALL_DIR
+	String tumor_name
+	String normal_name
+	String docker
+	String cluster_config
+
+	String fasta
+	File corealigner_bam
+	File corealigner_bam_index
+	String dbsnp
+	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 ${corealigner_bam} --algo TNhaplotyper --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}.TNseq.TN.vcf
+		
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File TNseq_vcf= "${sample}.TNseq.TN.vcf"
+		File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx"
+	}
+
+}
+
+

tasks/corealigner.wdl

@@ -0,0 +1,44 @@
+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

@@ -0,0 +1,37 @@
+task deduped_Metrics {
+
+    File ref_dir
+    
+	String SENTIEON_INSTALL_DIR
+	String sample
+	String fasta
+	File Dedup_bam
+	File Dedup_bam_index
+	String docker
+	String cluster_config
+	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 ${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 ${sample}_deduped_is_metrics.txt
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" 
+	}
+
+	output {
+		File deduped_coverage_metrics_sample_summary = "${sample}_deduped_coverage_metrics.sample_summary"
+		File deduped_coverage_metrics_sample_statistics = "${sample}_deduped_coverage_metrics.sample_statistics"
+		File deduped_coverage_metrics_sample_interval_statistics = "${sample}_deduped_coverage_metrics.sample_interval_statistics"
+		File deduped_coverage_metrics_sample_cumulative_coverage_proportions = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_proportions"
+		File deduped_coverage_metrics_sample_cumulative_coverage_counts = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_counts"
+	}
+}

tasks/gVCF_chromo_split.wdl

@@ -0,0 +1,109 @@
+task gVCF_chromo_split {
+	
+	File gvcf
+	File gvcf_idx
+	String SENTIEON_INSTALL_DIR
+	String sample
+	String docker
+	String cluster_config
+	String disk_size
+	
+
+	command <<<
+		cat ${gvcf} | grep '#' > header
+		for i in chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX
+		do
+			cat ${gvcf} | grep -v '#' | grep -w $i | cat header -  > ${sample}.$i.vcf
+		done
+
+		set -o pipefail
+		set -e
+		export SENTIEON_LICENSE=192.168.0.55:8990
+		nt=$(nproc)	
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr1.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr2.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr3.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr4.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr5.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr6.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr7.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr8.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr9.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr10.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr11.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr12.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr13.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr14.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr15.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr16.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr17.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr18.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr19.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr20.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr21.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr22.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chrX.vcf
+
+
+		>>>
+
+		runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File chr1_gvcf = "${sample}.chr1.vcf"
+		File chr2_gvcf = "${sample}.chr2.vcf"
+		File chr3_gvcf = "${sample}.chr3.vcf"
+		File chr4_gvcf = "${sample}.chr4.vcf"
+		File chr5_gvcf = "${sample}.chr5.vcf"
+		File chr6_gvcf = "${sample}.chr6.vcf"
+		File chr7_gvcf = "${sample}.chr7.vcf"
+		File chr8_gvcf = "${sample}.chr8.vcf"
+		File chr9_gvcf = "${sample}.chr9.vcf"
+		File chr10_gvcf = "${sample}.chr10.vcf"
+		File chr11_gvcf = "${sample}.chr11.vcf"
+		File chr12_gvcf = "${sample}.chr12.vcf"
+		File chr13_gvcf = "${sample}.chr13.vcf"
+		File chr14_gvcf = "${sample}.chr14.vcf"
+		File chr15_gvcf = "${sample}.chr15.vcf"
+		File chr16_gvcf = "${sample}.chr16.vcf"
+		File chr17_gvcf = "${sample}.chr17.vcf"
+		File chr18_gvcf = "${sample}.chr18.vcf"
+		File chr19_gvcf = "${sample}.chr19.vcf"
+		File chr20_gvcf = "${sample}.chr20.vcf"
+		File chr21_gvcf = "${sample}.chr21.vcf"
+		File chr22_gvcf = "${sample}.chr22.vcf"
+		File chrX_gvcf = "${sample}.chrX.vcf"
+		File chr1_gvcf_idx = "${sample}.chr1.vcf.idx"
+		File chr2_gvcf_idx = "${sample}.chr2.vcf.idx"
+		File chr3_gvcf_idx = "${sample}.chr3.vcf.idx"
+		File chr4_gvcf_idx = "${sample}.chr4.vcf.idx"
+		File chr5_gvcf_idx = "${sample}.chr5.vcf.idx"
+		File chr6_gvcf_idx = "${sample}.chr6.vcf.idx"
+		File chr7_gvcf_idx = "${sample}.chr7.vcf.idx"
+		File chr8_gvcf_idx = "${sample}.chr8.vcf.idx"
+		File chr9_gvcf_idx = "${sample}.chr9.vcf.idx"
+		File chr10_gvcf_idx = "${sample}.chr10.vcf.idx"
+		File chr11_gvcf_idx = "${sample}.chr11.vcf.idx"
+		File chr12_gvcf_idx = "${sample}.chr12.vcf.idx"
+		File chr13_gvcf_idx = "${sample}.chr13.vcf.idx"
+		File chr14_gvcf_idx = "${sample}.chr14.vcf.idx"
+		File chr15_gvcf_idx = "${sample}.chr15.vcf.idx"
+		File chr16_gvcf_idx = "${sample}.chr16.vcf.idx"
+		File chr17_gvcf_idx = "${sample}.chr17.vcf.idx"
+		File chr18_gvcf_idx = "${sample}.chr18.vcf.idx"
+		File chr19_gvcf_idx = "${sample}.chr19.vcf.idx"
+		File chr20_gvcf_idx = "${sample}.chr20.vcf.idx"
+		File chr21_gvcf_idx = "${sample}.chr21.vcf.idx"
+		File chr22_gvcf_idx = "${sample}.chr22.vcf.idx"
+		File chrX_gvcf_idx = "${sample}.chrX.vcf.idx"
+	}
+}
+
+
+
+

tasks/mapping.wdl

@@ -0,0 +1,34 @@
+task mapping {
+
+    File ref_dir
+    String fasta
+	File fastq_1
+	File fastq_2
+
+	String SENTIEON_INSTALL_DIR
+	String group
+	String sample
+	String pl
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e	
+		export SENTIEON_LICENSE=192.168.0.55:8990
+		nt=$(nproc)
+		${SENTIEON_INSTALL_DIR}/bin/bwa mem -M -R "@RG\tID:${group}\tSM:${sample}\tPL:${pl}" -t $nt -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} | ${SENTIEON_INSTALL_DIR}/bin/sentieon util sort -o ${sample}.sorted.bam -t $nt --sam2bam -i -
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File sorted_bam = "${sample}.sorted.bam"
+		File sorted_bam_index = "${sample}.sorted.bam.bai"
+	}
+}

workflow.wdl

@@ -0,0 +1,75 @@
+import "./tasks/gVCF_chromo_split.wdl" as gVCF_chromo_split
+import "./tasks/GVCFtyper_chr3.wdl" as GVCFtyper_chr3
+import "./tasks/GVCFtyper_chr4.wdl" as GVCFtyper_chr4
+import "./tasks/GVCFtyper_chr7.wdl" as GVCFtyper_chr7
+import "./tasks/GVCFtyper_chr8.wdl" as GVCFtyper_chr8
+import "./tasks/GVCFtyper_chrX.wdl" as GVCFtyper_chrX
+
+workflow {{ project_name }} {
+
+	String gvcf_dir
+	String SENTIEON_INSTALL_DIR
+	String docker
+	String project
+	String fasta
+	File ref_dir
+	String disk_size
+	String cluster_config
+
+
+	call GVCFtyper_chr3.GVCFtyper_chr3 as GVCFtyper_chr3 {
+		input:
+		ref_dir=ref_dir,
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		fasta=fasta,
+		gvcf_dir=gvcf_dir,
+		project=project,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+	call GVCFtyper_chr4.GVCFtyper_chr4 as GVCFtyper_chr4 {
+		input:
+		ref_dir=ref_dir,
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		fasta=fasta,
+		gvcf_dir=gvcf_dir,
+		project=project,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+	call GVCFtyper_chr7.GVCFtyper_chr7 as GVCFtyper_chr7 {
+		input:
+		ref_dir=ref_dir,
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		fasta=fasta,
+		gvcf_dir=gvcf_dir,
+		project=project,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+	call GVCFtyper_chr8.GVCFtyper_chr8 as GVCFtyper_chr8 {
+		input:
+		ref_dir=ref_dir,
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		fasta=fasta,
+		gvcf_dir=gvcf_dir,
+		project=project,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+	call GVCFtyper_chrX.GVCFtyper_chrX as GVCFtyper_chrX {
+		input:
+		ref_dir=ref_dir,
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		fasta=fasta,
+		gvcf_dir=gvcf_dir,
+		project=project,
+		docker=docker,
+		cluster_config=cluster_config,
+		disk_size=disk_size
+	}
+}