first commit

README.md

+> Author : Yechao Huang
+>
+>
+> E-mail：[1721070009@fudan.edu.cn](mailto:1721070009@fudan.edu.cn)
+>
+> Git: <http://choppy.3steps.cn/huangyechao/wes-germline.git>
+>
+> Last Updates: 06/02/2019
+
+## 简介
+
+`wes-germline`是根据 [Sentieon](https://support.sentieon.com/manual/) 软件全外显子组`Germline`突变数据分析推荐流程所构建的 [Choppy-pipe](http://choppy.3steps.cn/) 系统的 APP。利用该 APP 可以获得从全外显子组测序原始文件`fastq` 到包含`Germline`突变信息的`vcf`文件的整个过程。主要包括数据的预处理、中间数据质控以及变异的检测。
+
+## 快速安装
+
+#### Requirements
+
+- Python 3
+- [choppy](http://choppy.3steps.cn/)
+- Ali-Cloud
+
+在终端中输入以下命令即可快速安装本APP。
+
+```bash
+$ source activate choppy
+$ choppy install huangyechao/wes-germline-latest
+$ choppy apps
+```
+
+## 使用方法
+
+### 任务准备
+
+按照上述步骤安装成功之后，可以通过下面简单的命令即可使用APP：
+
+```bash
+# Generate samples file
+$ choppy samples huangyechao/wes-germline-latest --out samples.csv
+```
+
+`sample.csv` 包含以下几个需要填写的参数：
+
+``` bash
+read1,read2,sample_name,cluster,sample_id,disk_size,regions
+# read1  		双端测序数据的R1端在阿里云上的路径信息
+# read2  		双端测序数据的R2端在阿里云上的路径信息
+# sample_name	输出文件名的前缀
+# regions		全外显子组测序时测序区域的bed文件
+# cluster		使用的机器类型，不填则默认使用 OnDemand ecs.sn1ne.4xlarge img-ubuntu-vpc
+# sample_id		每个样本任务的识别码。注意：同一个samples文件中，不同样本的ID应该不同
+# disk_size		任务运行时，集群存储空间设置
+```
+
+> 机器类型选择可以参照：[计算网络增强型实例规格族sn1ne](https://help.aliyun.com/document_detail/25378.html?spm=a2c4g.11186623.2.11.1a3d6b46rNmksN#sn1ne) 以及 [bcs](https://help.aliyun.com/document_detail/42391.html?spm=5176.10695662.1996646101.searchclickresult.5c0b12b5Adk9Xc) 类型机器，对于全外显子组数据不要使用小于32CPU的机器类型
+
+### 任务提交
+
+在配置好`samples.csv` 文件后，使用以下命令可以提交计算任务：
+
+```bash
+$ choppy batch huangyechao/wes-germline-latest sample.csv --project-name Your_project_name
+```
+
+提交成功后，即可在工作目录下找到生成的目录名为Your_project_name，里面包含了本次提交任务的所有样本信息。
+
+### 任务输出
+
+任务成功结束后，便可以在阿里云相应的OSS端生成相应的结果文件。包括数据预处理产生的中间结果文件以及变异检测得到的`vcf`文件。
+
+## 流程示意图
+
+![](assets/wes.png)
+
+
+
+### 输出文件说明
+
+整个分析流程中，每个步骤输出的结果说明如下：
+
+- **call-mapping** 原始数据经过比对后生成的排序后的`sample.sorted.bam`文件及其索引文件
+- **call-Metrics** 比对后生成的`sample.sorted.bam`文件的质控信息
+- **call-Dedup** 比对的结果去除重复后的`sample.sorted.deduped.bam`文件及其索引文件
+- **call-deduped_Metrics** 去除重复后的`sample.sorted.deduped.bam` 文件的质控信息
+- **call-Realigner** 去除重复后重比对的`sample.sorted.deduped.realigned.bam`文件及其索引文件
+- **call-BQSR** 局部碱基矫正的`sample.sorted.deduped.realigned.recaled.bam`文件、索引文件及其相关信息
+- **call-Haplotyper** 变异检测得到的`sample.vcf`文件及其索引文件
+
+### 软件版本及参数
+
+| 软件/文件           | 版本                                          |
+| :------------------ | --------------------------------------------- |
+| Sentieon            | v2018.08.01                                   |
+| 参考基因组（fasta） | GRCh38.d1.vd1.fa                              |
+| dbsnp               | dbsnp_146.hg38.vcf                            |
+| db_mills            | Mills_and_1000G_gold_standard.indels.hg38.vcf |
+
+
+
+### 附录
+
+
+
+### 参考文献
+

inputs

+{
+  "{{ project_name }}.fasta": "hg19_nochr.fa",
+  "{{ project_name }}.ref_dir": "oss://pgx-reference-data/hg19/",
+  "{{ project_name }}.dbsnp": "dbsnp_138.hg19_nochr_sorted.vcf",
+  "{{ project_name }}.fastq_1": "{{ read1 }}",
+  "{{ project_name }}.SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
+  "{{ project_name }}.dbmills_dir": "oss://pgx-reference-data/hg19/",
+  "{{ project_name }}.db_mills": "Mills_and_1000G_gold_standard.indels.hg19_nochr.vcf",
+  "{{ project_name }}.cluster_config": "{{ cluster if cluster != '' else 'OnDemand ecs.sn1ne.4xlarge img-ubuntu-vpc' }}",
+  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
+  "{{ project_name }}.dbsnp_dir": "oss://pgx-reference-data/hg19/",
+  "{{ project_name }}.sample": "{{ sample_name }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}", 
+  "{{ project_name }}.regions": "{{ regions }}",
+  "{{ project_name }}.fastq_2": "{{ read2 }}"
+}
+

tasks/BQSR.wdl

+task BQSR {
+	
+    File ref_dir
+    File dbsnp_dir
+    File dbmills_dir
+    
+	String sample
+	String SENTIEON_INSTALL_DIR
+	String fasta
+	File regions
+	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} --interval ${regions} --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

+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/Haplotyper.wdl

+task Haplotyper {
+	
+    File ref_dir
+    File dbsnp_dir
+    
+	String SENTIEON_INSTALL_DIR
+	String fasta
+	File recaled_bam
+	File recaled_bam_index
+	File regions
+	String dbsnp
+	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 --interval ${regions} -r ${ref_dir}/${fasta} -t $nt -i ${recaled_bam} --algo Haplotyper -d ${dbsnp_dir}/${dbsnp} ${sample}_hc.vcf
+	>>>
+	
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File vcf = "${sample}_hc.vcf"
+		File vcf_idx = "${sample}_hc.vcf.idx"
+	}
+}
+
+

tasks/Metrics.wdl

+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

+task Realigner {
+
+    File ref_dir
+    File dbmills_dir
+
+	String SENTIEON_INSTALL_DIR
+	String sample
+	String fasta
+
+	File regions
+	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} --interval_list ${regions} ${sample}.sorted.deduped.realigned.bam
+	
+	>>>
+
+	runtime {
+		docker:docker
+    	cluster: cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File realigner_bam = "${sample}.sorted.deduped.realigned.bam"
+		File realigner_bam_index = "${sample}.sorted.deduped.realigned.bam.bai"
+
+	}
+}
+
+

tasks/TNscope.wdl

+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

+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

+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
+    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/mapping.wdl

+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

+import "./tasks/mapping.wdl" as mapping
+import "./tasks/Metrics.wdl" as Metrics
+import "./tasks/Dedup.wdl" as Dedup
+import "./tasks/deduped_Metrics.wdl" as deduped_Metrics
+import "./tasks/Realigner.wdl" as Realigner
+import "./tasks/BQSR.wdl" as BQSR
+import "./tasks/Haplotyper.wdl" as Haplotyper
+
+
+workflow {{ project_name }} {
+
+	File fastq_1
+	File fastq_2
+
+	String SENTIEON_INSTALL_DIR
+	String sample
+	String docker
+	
+	String fasta
+	File ref_dir
+	File dbmills_dir
+	String db_mills
+	File dbsnp_dir
+	File regions
+	String dbsnp
+	String disk_size
+	String cluster_config
+
+
+	call mapping.mapping as mapping {
+		input: 
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		group=sample,
+		sample=sample,
+		pl="ILLUMINAL",
+		fasta=fasta,
+		ref_dir=ref_dir,
+		fastq_1=fastq_1,
+		fastq_2=fastq_2,
+		docker=docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+
+	call Metrics.Metrics as Metrics {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		fasta=fasta,
+		ref_dir=ref_dir,
+		sorted_bam=mapping.sorted_bam,
+		sorted_bam_index=mapping.sorted_bam_index,		
+		sample=sample,
+		docker=docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+
+	call Dedup.Dedup as Dedup {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		sorted_bam=mapping.sorted_bam,
+		sorted_bam_index=mapping.sorted_bam_index,
+		sample=sample,
+		docker=docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+	call deduped_Metrics.deduped_Metrics as deduped_Metrics {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		fasta=fasta,
+		ref_dir=ref_dir,
+		Dedup_bam=Dedup.Dedup_bam,
+		Dedup_bam_index=Dedup.Dedup_bam_index,
+		sample=sample,
+		docker=docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+	call Realigner.Realigner as Realigner {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		fasta=fasta,
+		ref_dir=ref_dir,
+		Dedup_bam=Dedup.Dedup_bam,
+		Dedup_bam_index=Dedup.Dedup_bam_index,
+		db_mills=db_mills,
+		dbmills_dir=dbmills_dir,
+		sample=sample,
+		docker=docker,
+		disk_size=disk_size,
+		regions=regions,
+		cluster_config=cluster_config
+	}
+
+	call BQSR.BQSR as BQSR {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		fasta=fasta,
+		ref_dir=ref_dir,
+		realigned_bam=Realigner.realigner_bam,
+		realigned_bam_index=Realigner.realigner_bam_index,
+		db_mills=db_mills,
+		dbmills_dir=dbmills_dir,
+		dbsnp=dbsnp,
+		dbsnp_dir=dbsnp_dir,
+		sample=sample,
+		regions=regions,
+		docker=docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+	call Haplotyper.Haplotyper as Haplotyper {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		fasta=fasta,
+		ref_dir=ref_dir,
+		recaled_bam=BQSR.recaled_bam,
+		recaled_bam_index=BQSR.recaled_bam_index,
+		dbsnp=dbsnp,
+		dbsnp_dir=dbsnp_dir,
+		sample=sample,
+		regions=regions,
+		docker=docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+}