Update: README.md

README.md

@@ -1,22 +1,32 @@
-# README.md
+#### Introduction
+This APP developed for somatic short variant discovery (SNVs + Indels).
 
-> Author: Yaqing Liu
-> 
-> Email: [yaqing.liu@outlook.com](mailto:yaqing.liu@outlook.com)
-> 
-> Last Updates: 25/04/2021
+Supported callers:
+* TNhaplotyper2
+* TNscope
+* VarScan
+* TNhaplotyper (This caller is only available in `v0.1.0` as it is too outdated)
+Variant caller can be selected by setting `ture/false` in the submitted sample.csv.
 
-#### Requirements
+Types of data that can be received:
+* TN matched WES
+* WGS
+The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs).
 
-- choppy
-- Ali-Cloud
-- Linux
+**New version**
+* The TNhaplotyper, also named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2.
+* The `corealigner` step has been removed.
 
-#### Introduction
-Variant calling pipeline from mapping to generating MAF files with three optional callers, i.e. TNseq, TNscope and Varscan2, for WGS and WES data.
+**Please carefully check**
+* the reference genome
+* bed file
+* the caller you want to use
+* whether PoN needs to be set
+
+#### How to run this APP
+
+We recommend using choppy system and Aliyun OSS service. The command will look like this:
 
-**Please carefully check the reference genome, bed file, etc.**
-#### Usage
 ```
 open-choppy-env
 
@@ -29,4 +39,9 @@ choppy batch YaqingLiu/variant-calling-latest samples.csv -p Project -l Label
 
 # Query the status of all tasks in the project
 choppy query -L Label | grep "status"
-```
+```
+
+**Please note**
+The `defaults` can be forcibly replaced by the settings in `samples.csv`.
+
+Therefore, there is no need to contact me over this issue.

defaults

@@ -7,6 +7,7 @@
     "SENTIEON_LICENSE": "192.168.0.55:8990",
     "dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
     "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
+    "germline_resource": "oss://pgx-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz",
     "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2020.10.07",
     "varscan_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/varscan2:v2.4.3",
     "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2018.04",

inputs

@@ -12,6 +12,7 @@
   "{{ project_name }}.SENTIEON_LICENSE": "{{ SENTIEON_LICENSE }}",
   "{{ project_name }}.dbmills_dir": "{{ dbmills_dir }}",
   "{{ project_name }}.db_mills": "{{ db_mills }}",
+  "{{ project_name }}.germline_resource": "{{ germline_resource }}",
   "{{ project_name }}.sentieon_docker": "{{ sentieon_docker }}",
   "{{ project_name }}.varscan_docker": "{{ varscan_docker }}",
   "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",

tasks/PON.wdl

@@ -1,41 +0,0 @@
-task PON {
-
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	String sample
-
-	File ref_dir
-	String fasta
-	File cosmic_dir
-	String cosmic_vcf
-	File dbsnp_dir
-	String dbsnp
-
-	File normal_recaled_bam
-	File normal_recaled_bam_index
-	String docker
-	String cluster_config
-	String disk_size
-	
-	command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-		nt=$(nproc)
-		mkdir -p /cromwell_root/tmp/cosmic/
-		cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/cosmic/
-		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/cosmic/${cosmic_vcf}
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${normal_recaled_bam} --algo TNhaplotyper --detect_pon --cosmic /cromwell_root/tmp/cosmic/${cosmic_vcf} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}_pon.vcf
-	>>>
-	
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"	
-	}
-
-	output {
-		File pon_vcf = "${sample}_pon.vcf"
-	}
-}

tasks/TNhaplotyper2.wdl

@@ -0,0 +1,72 @@
+task TNhaplotyper2 {
+	File ref_dir
+	File dbsnp_dir
+	String sample
+	String SENTIEON_INSTALL_DIR
+	String SENTIEON_LICENSE
+	String tumor_name
+	String normal_name
+	String docker
+	String cluster_config
+
+	String fasta
+	File germline_resource
+	File tumor_recaled_bam
+	File tumor_recaled_bam_index
+	File tumor_recal_table
+	File normal_recaled_bam
+	File normal_recaled_bam_index
+	File normal_recal_table
+	File TNhaplotyper2_PoN
+	String dbsnp
+	String disk_size
+	File regions
+
+	command <<<
+		set -o pipefail
+		set -e
+		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+		nt=$(nproc)
+
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${corealigner_bam} --algo TNhaplotyper2 --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}.TNhaplotyper2.TN.vcf
+
+
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} \
+		-i ${tumor_recaled_bam} -q ${tumor_recal_table} \
+		-i ${normal_recaled_bam} -q ${normal_recal_table} \
+		--algo TNhaplotyper2 --tumor_sample ${tumor_name} \
+		--normal_sample ${normal_name} \
+		--germline_vcf ${germline_resource} \
+		--pon ${TNhaplotyper2_PoN} \
+		${sample}.TNhaplotyper2.TN.tmp.vcf \
+		--algo OrientationBias --tumor_sample ${tumor_name} \
+		ORIENTATION_DATA \
+		--algo ContaminationModel --tumor_sample ${tumor_name} \
+		--normal_sample ${normal_name} \
+		--vcf ${germline_resource} \
+		--tumor_segments CONTAMINATION_DATA.segments \
+		CONTAMINATION_DATA
+		
+		sentieon driver -r REFERENCE \
+		--algo TNfilter --tumor_sample ${tumor_name} \
+		--normal_sample ${normal_name} \
+		-v ${sample}.TNhaplotyper2.TN.tmp.vcf \
+		--contamination CONTAMINATION_DATA \
+		--tumor_segments CONTAMINATION_DATA.segments \
+		--orientation_priors ORIENTATION_DATA \
+		${sample}.TNhaplotyper2.TN.vcf
+	>>>
+
+	runtime {
+		docker: docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File TNhaplotyper2_vcf= "${sample}.TNhaplotyper2.TN.vcf"
+		File TNhaplotyper2_vcf_index = "${sample}.TNhaplotyper2.TN.vcf.idx"
+	}
+
+}

workflow.wdl

@@ -6,7 +6,6 @@ import "./tasks/Realigner.wdl" as Realigner
 import "./tasks/BQSR.wdl" as BQSR
 import "./tasks/Haplotyper.wdl" as Haplotyper
 import "./tasks/corealigner.wdl" as corealigner
-import "./tasks/PON.wdl" as PON
 import "./tasks/TNseq.wdl" as TNseq
 import "./tasks/TNscope.wdl" as TNscope
 import "./tasks/somatic.wdl" as somatic
@@ -17,467 +16,468 @@ import "./tasks/vcf2maf.wdl" as vcf2maf
 
 
 workflow {{ project_name }} {
-	
-	String sample_id
-	File tumor_fastq_1
-	File tumor_fastq_2
-	File normal_fastq_1
-	File normal_fastq_2
+    
+    String sample_id
+    File tumor_fastq_1
+    File tumor_fastq_2
+    File normal_fastq_1
+    File normal_fastq_2
 
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	String sentieon_docker
-	String varscan_docker
-	String annovar_docker
-	String maftools_docker
-	
-	File ref_dir
-	String fasta
-	File dbmills_dir
-	String db_mills
-	File dbsnp_dir
-	String dbsnp
-	File? regions
-	File database
-	String disk_size
-	String cluster_config
+    String SENTIEON_INSTALL_DIR
+    String SENTIEON_LICENSE
+    String sentieon_docker
+    String varscan_docker
+    String annovar_docker
+    String maftools_docker
+    
+    File ref_dir
+    String fasta
+    File dbmills_dir
+    String db_mills
+    File dbsnp_dir
+    String dbsnp
+    File germline_resource
+    File? regions
+    File database
+    String disk_size
+    String cluster_config
 
-	Boolean set_pon
-	File? pon_vcf
-	File? cosmic_dir
-	String? cosmic_vcf
+    Boolean set_pon
+    File? pon_vcf
+    File? cosmic_dir
+    String? cosmic_vcf
 
-	Boolean germline
-	Boolean tnseq
-	Boolean tnscope
-	Boolean varscan
+    Boolean germline
+    Boolean tnseq
+    Boolean tnscope
+    Boolean varscan
 
 
-	call mapping.mapping as tumor_mapping {
-		input: 
-		group=sample_id + '_tumor',
-		sample=sample_id + '_tumor',
-		fastq_1=tumor_fastq_1,
-		fastq_2=tumor_fastq_2,
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		pl="ILLUMINAL",
-		fasta=fasta,
-		ref_dir=ref_dir,
-		docker=sentieon_docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
+    call mapping.mapping as tumor_mapping {
+        input: 
+        group=sample_id + '_tumor',
+        sample=sample_id + '_tumor',
+        fastq_1=tumor_fastq_1,
+        fastq_2=tumor_fastq_2,
+        SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+        SENTIEON_LICENSE=SENTIEON_LICENSE,
+        pl="ILLUMINAL",
+        fasta=fasta,
+        ref_dir=ref_dir,
+        docker=sentieon_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_config
+    }
 
-	call Metrics.Metrics as tumor_Metrics {
-		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		fasta=fasta,
-		ref_dir=ref_dir,
-		sorted_bam=tumor_mapping.sorted_bam,
-		sorted_bam_index=tumor_mapping.sorted_bam_index,
-		sample=sample_id + '_tumor',
-		docker=sentieon_docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
+    call Metrics.Metrics as tumor_Metrics {
+        input:
+        SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+        SENTIEON_LICENSE=SENTIEON_LICENSE,
+        fasta=fasta,
+        ref_dir=ref_dir,
+        sorted_bam=tumor_mapping.sorted_bam,
+        sorted_bam_index=tumor_mapping.sorted_bam_index,
+        sample=sample_id + '_tumor',
+        docker=sentieon_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_config
+    }
 
-	call Dedup.Dedup as tumor_Dedup {
-		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		sorted_bam=tumor_mapping.sorted_bam,
-		sorted_bam_index=tumor_mapping.sorted_bam_index,
-		sample=sample_id + '_tumor',
-		docker=sentieon_docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
+    call Dedup.Dedup as tumor_Dedup {
+        input:
+        SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+        SENTIEON_LICENSE=SENTIEON_LICENSE,
+        sorted_bam=tumor_mapping.sorted_bam,
+        sorted_bam_index=tumor_mapping.sorted_bam_index,
+        sample=sample_id + '_tumor',
+        docker=sentieon_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_config
+    }
 
-	call deduped_Metrics.deduped_Metrics as tumor_deduped_Metrics {
-		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		fasta=fasta,
-		ref_dir=ref_dir,
-		Dedup_bam=tumor_Dedup.Dedup_bam,
-		Dedup_bam_index=tumor_Dedup.Dedup_bam_index,
-		sample=sample_id + '_tumor',
-		docker=sentieon_docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
+    call deduped_Metrics.deduped_Metrics as tumor_deduped_Metrics {
+        input:
+        SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+        SENTIEON_LICENSE=SENTIEON_LICENSE,
+        fasta=fasta,
+        ref_dir=ref_dir,
+        Dedup_bam=tumor_Dedup.Dedup_bam,
+        Dedup_bam_index=tumor_Dedup.Dedup_bam_index,
+        sample=sample_id + '_tumor',
+        docker=sentieon_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_config
+    }
 
-	call Realigner.Realigner as tumor_Realigner {
-		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		fasta=fasta,
-		ref_dir=ref_dir,
-		Dedup_bam=tumor_Dedup.Dedup_bam,
-		Dedup_bam_index=tumor_Dedup.Dedup_bam_index,
-		db_mills=db_mills,
-		dbmills_dir=dbmills_dir,
-		sample=sample_id + '_tumor',
-		docker=sentieon_docker,
-		disk_size=disk_size,
-		regions=regions,
-		cluster_config=cluster_config
-	}
+    call Realigner.Realigner as tumor_Realigner {
+        input:
+        SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+        SENTIEON_LICENSE=SENTIEON_LICENSE,
+        fasta=fasta,
+        ref_dir=ref_dir,
+        Dedup_bam=tumor_Dedup.Dedup_bam,
+        Dedup_bam_index=tumor_Dedup.Dedup_bam_index,
+        db_mills=db_mills,
+        dbmills_dir=dbmills_dir,
+        sample=sample_id + '_tumor',
+        docker=sentieon_docker,
+        disk_size=disk_size,
+        regions=regions,
+        cluster_config=cluster_config
+    }
 
-	call BQSR.BQSR as tumor_BQSR {
-		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		fasta=fasta,
-		ref_dir=ref_dir,
-		realigned_bam=tumor_Realigner.realigner_bam,
-		realigned_bam_index=tumor_Realigner.realigner_bam_index,
-		db_mills=db_mills,
-		dbmills_dir=dbmills_dir,
-		dbsnp=dbsnp,
-		dbsnp_dir=dbsnp_dir,
-		sample=sample_id + '_tumor',
-		regions=regions,
-		docker=sentieon_docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
+    call BQSR.BQSR as tumor_BQSR {
+        input:
+        SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+        SENTIEON_LICENSE=SENTIEON_LICENSE,
+        fasta=fasta,
+        ref_dir=ref_dir,
+        realigned_bam=tumor_Realigner.realigner_bam,
+        realigned_bam_index=tumor_Realigner.realigner_bam_index,
+        db_mills=db_mills,
+        dbmills_dir=dbmills_dir,
+        dbsnp=dbsnp,
+        dbsnp_dir=dbsnp_dir,
+        sample=sample_id + '_tumor',
+        regions=regions,
+        docker=sentieon_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_config
+    }
 
-	call mapping.mapping as normal_mapping {
-		input: 
-		group=sample_id + '_normal',
-		sample=sample_id + '_normal',
-		fastq_1=normal_fastq_1,
-		fastq_2=normal_fastq_2,
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		pl="ILLUMINAL",
-		fasta=fasta,
-		ref_dir=ref_dir,
-		docker=sentieon_docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
+    call mapping.mapping as normal_mapping {
+        input: 
+        group=sample_id + '_normal',
+        sample=sample_id + '_normal',
+        fastq_1=normal_fastq_1,
+        fastq_2=normal_fastq_2,
+        SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+        SENTIEON_LICENSE=SENTIEON_LICENSE,
+        pl="ILLUMINAL",
+        fasta=fasta,
+        ref_dir=ref_dir,
+        docker=sentieon_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_config
+    }
 
-	call Metrics.Metrics as normal_Metrics {
-		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		fasta=fasta,
-		ref_dir=ref_dir,
-		sorted_bam=normal_mapping.sorted_bam,
-		sorted_bam_index=normal_mapping.sorted_bam_index,
-		sample=sample_id + '_normal',
-		docker=sentieon_docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
+    call Metrics.Metrics as normal_Metrics {
+        input:
+        SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+        SENTIEON_LICENSE=SENTIEON_LICENSE,
+        fasta=fasta,
+        ref_dir=ref_dir,
+        sorted_bam=normal_mapping.sorted_bam,
+        sorted_bam_index=normal_mapping.sorted_bam_index,
+        sample=sample_id + '_normal',
+        docker=sentieon_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_config
+    }
 
-	call Dedup.Dedup as normal_Dedup {
-		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		sorted_bam=normal_mapping.sorted_bam,
-		sorted_bam_index=normal_mapping.sorted_bam_index,
-		sample=sample_id + '_normal',
-		docker=sentieon_docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
+    call Dedup.Dedup as normal_Dedup {
+        input:
+        SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+        SENTIEON_LICENSE=SENTIEON_LICENSE,
+        sorted_bam=normal_mapping.sorted_bam,
+        sorted_bam_index=normal_mapping.sorted_bam_index,
+        sample=sample_id + '_normal',
+        docker=sentieon_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_config
+    }
 
-	call deduped_Metrics.deduped_Metrics as normal_deduped_Metrics {
-		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		fasta=fasta,
-		ref_dir=ref_dir,
-		Dedup_bam=normal_Dedup.Dedup_bam,
-		Dedup_bam_index=normal_Dedup.Dedup_bam_index,
-		sample=sample_id + '_normal',
-		docker=sentieon_docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
+    call deduped_Metrics.deduped_Metrics as normal_deduped_Metrics {
+        input:
+        SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+        SENTIEON_LICENSE=SENTIEON_LICENSE,
+        fasta=fasta,
+        ref_dir=ref_dir,
+        Dedup_bam=normal_Dedup.Dedup_bam,
+        Dedup_bam_index=normal_Dedup.Dedup_bam_index,
+        sample=sample_id + '_normal',
+        docker=sentieon_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_config
+    }
 
-	call Realigner.Realigner as normal_Realigner {
-		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		fasta=fasta,
-		ref_dir=ref_dir,
-		Dedup_bam=normal_Dedup.Dedup_bam,
-		Dedup_bam_index=normal_Dedup.Dedup_bam_index,
-		db_mills=db_mills,
-		dbmills_dir=dbmills_dir,
-		sample=sample_id + '_normal',
-		docker=sentieon_docker,
-		disk_size=disk_size,
-		regions=regions,
-		cluster_config=cluster_config
-	}
+    call Realigner.Realigner as normal_Realigner {
+        input:
+        SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+        SENTIEON_LICENSE=SENTIEON_LICENSE,
+        fasta=fasta,
+        ref_dir=ref_dir,
+        Dedup_bam=normal_Dedup.Dedup_bam,
+        Dedup_bam_index=normal_Dedup.Dedup_bam_index,
+        db_mills=db_mills,
+        dbmills_dir=dbmills_dir,
+        sample=sample_id + '_normal',
+        docker=sentieon_docker,
+        disk_size=disk_size,
+        regions=regions,
+        cluster_config=cluster_config
+    }
 
-	call BQSR.BQSR as normal_BQSR {
-		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		fasta=fasta,
-		ref_dir=ref_dir,
-		realigned_bam=normal_Realigner.realigner_bam,
-		realigned_bam_index=normal_Realigner.realigner_bam_index,
-		db_mills=db_mills,
-		dbmills_dir=dbmills_dir,
-		dbsnp=dbsnp,
-		dbsnp_dir=dbsnp_dir,
-		sample=sample_id + '_normal',
-		regions=regions,
-		docker=sentieon_docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
+    call BQSR.BQSR as normal_BQSR {
+        input:
+        SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+        SENTIEON_LICENSE=SENTIEON_LICENSE,
+        fasta=fasta,
+        ref_dir=ref_dir,
+        realigned_bam=normal_Realigner.realigner_bam,
+        realigned_bam_index=normal_Realigner.realigner_bam_index,
+        db_mills=db_mills,
+        dbmills_dir=dbmills_dir,
+        dbsnp=dbsnp,
+        dbsnp_dir=dbsnp_dir,
+        sample=sample_id + '_normal',
+        regions=regions,
+        docker=sentieon_docker,
+        disk_size=disk_size,
+        cluster_config=cluster_config
+    }
 
-	if (germline) {
-		call Haplotyper.Haplotyper as Haplotyper {
-			input:
-			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			sample=sample_id + '_normal',
-			fasta=fasta,
-			ref_dir=ref_dir,
-			recaled_bam=normal_BQSR.recaled_bam,
-			recaled_bam_index=normal_BQSR.recaled_bam_index,
-			dbsnp=dbsnp,
-			dbsnp_dir=dbsnp_dir,
-			regions=regions,
-			docker=sentieon_docker,
-			disk_size=disk_size,
-			cluster_config=cluster_config
-		}
-	}
-	
-	call corealigner.corealigner as corealigner {
-		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		SENTIEON_LICENSE=SENTIEON_LICENSE,
-		fasta=fasta,
-		ref_dir=ref_dir,
-		sample=sample_id,
-		docker=sentieon_docker,
-		db_mills=db_mills,
-		dbmills_dir=dbmills_dir,
-		dbsnp=dbsnp,
-		dbsnp_dir=dbsnp_dir,
-		tumor_recaled_bam=tumor_BQSR.recaled_bam,
-		tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
-		normal_recaled_bam=normal_BQSR.recaled_bam,
-		normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
-		disk_size=disk_size,
-		cluster_config=cluster_config
-	}
-	
-	if (tnseq) {
-		call TNseq.TNseq as TNseq {
-			input:
-			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			fasta=fasta,
-			ref_dir=ref_dir,
-			regions=regions,
-			corealigner_bam=corealigner.corealigner_bam,
-			corealigner_bam_index=corealigner.corealigner_bam_index,
-			dbsnp=dbsnp,
-			dbsnp_dir=dbsnp_dir,
-			set_pon=set_pon,
-			pon_vcf=pon_vcf,
-			cosmic_vcf=cosmic_vcf,
-			cosmic_dir=cosmic_dir,
-			tumor_name=sample_id + "_tumor",
-			normal_name=sample_id + "_normal",
-			docker=sentieon_docker,
-			sample=sample_id,
-			disk_size=disk_size,
-			cluster_config=cluster_config
-		}
+    if (germline) {
+        call Haplotyper.Haplotyper as Haplotyper {
+            input:
+            SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+            SENTIEON_LICENSE=SENTIEON_LICENSE,
+            sample=sample_id + '_normal',
+            fasta=fasta,
+            ref_dir=ref_dir,
+            recaled_bam=normal_BQSR.recaled_bam,
+            recaled_bam_index=normal_BQSR.recaled_bam_index,
+            dbsnp=dbsnp,
+            dbsnp_dir=dbsnp_dir,
+            regions=regions,
+            docker=sentieon_docker,
+            disk_size=disk_size,
+            cluster_config=cluster_config
+        }
+    }
+    
+    call corealigner.corealigner as corealigner {
+        input:
+        SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+        SENTIEON_LICENSE=SENTIEON_LICENSE,
+        fasta=fasta,
+        ref_dir=ref_dir,
+        sample=sample_id,
+        docker=sentieon_docker,
+        db_mills=db_mills,
+        dbmills_dir=dbmills_dir,
+        dbsnp=dbsnp,
+        dbsnp_dir=dbsnp_dir,
+        tumor_recaled_bam=tumor_BQSR.recaled_bam,
+        tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
+        normal_recaled_bam=normal_BQSR.recaled_bam,
+        normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
+        disk_size=disk_size,
+        cluster_config=cluster_config
+    }
+    
+    if (tnseq) {
+        call TNseq.TNseq as TNseq {
+            input:
+            SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+            SENTIEON_LICENSE=SENTIEON_LICENSE,
+            fasta=fasta,
+            ref_dir=ref_dir,
+            regions=regions,
+            corealigner_bam=corealigner.corealigner_bam,
+            corealigner_bam_index=corealigner.corealigner_bam_index,
+            dbsnp=dbsnp,
+            dbsnp_dir=dbsnp_dir,
+            set_pon=set_pon,
+            pon_vcf=pon_vcf,
+            cosmic_vcf=cosmic_vcf,
+            cosmic_dir=cosmic_dir,
+            tumor_name=sample_id + "_tumor",
+            normal_name=sample_id + "_normal",
+            docker=sentieon_docker,
+            sample=sample_id,
+            disk_size=disk_size,
+            cluster_config=cluster_config
+        }
 
-		call annovar.annovar as TNseq_annovar {
-			input:
-			sample=sample_id,
-			vcf=TNseq.TNseq_vcf,
-			database=database,
-			docker=annovar_docker,
-			cluster_config=cluster_config,
-			disk_size=disk_size
-		}
+        call annovar.annovar as TNseq_annovar {
+            input:
+            sample=sample_id,
+            vcf=TNseq.TNseq_vcf,
+            database=database,
+            docker=annovar_docker,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+        }
 
-		call vcf2maf.vcf2maf as TNseq_vcf2maf {
-			input:
-			sample=sample_id,
-			multianno_txt=TNseq_annovar.multianno_txt,
-			docker=maftools_docker,
-			cluster_config=cluster_config,
-			disk_size=disk_size
-		}
-	}
+        call vcf2maf.vcf2maf as TNseq_vcf2maf {
+            input:
+            sample=sample_id,
+            multianno_txt=TNseq_annovar.multianno_txt,
+            docker=maftools_docker,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+        }
+    }
 
-	if (tnscope) {
-		call TNscope.TNscope as TNscope {
-			input:
-			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			fasta=fasta,
-			ref_dir=ref_dir,
-			regions=regions,
-			corealigner_bam=corealigner.corealigner_bam,
-			corealigner_bam_index=corealigner.corealigner_bam_index,
-			dbsnp=dbsnp,
-			dbsnp_dir=dbsnp_dir,
-			set_pon=set_pon,
-			pon_vcf=pon_vcf,
-			cosmic_vcf=cosmic_vcf,
-			cosmic_dir=cosmic_dir,
-			tumor_name=sample_id + "_tumor",
-			normal_name=sample_id + "_normal",
-			docker=sentieon_docker,
-			sample=sample_id,
-			disk_size=disk_size,
-			cluster_config=cluster_config
-		}
-		
-		call annovar.annovar as TNscope_annovar {
-			input:
-			sample=sample_id,
-			vcf=TNscope.TNscope_vcf,
-			database=database,
-			docker=annovar_docker,
-			cluster_config=cluster_config,
-			disk_size=disk_size
-		}
+    if (tnscope) {
+        call TNscope.TNscope as TNscope {
+            input:
+            SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+            SENTIEON_LICENSE=SENTIEON_LICENSE,
+            fasta=fasta,
+            ref_dir=ref_dir,
+            regions=regions,
+            corealigner_bam=corealigner.corealigner_bam,
+            corealigner_bam_index=corealigner.corealigner_bam_index,
+            dbsnp=dbsnp,
+            dbsnp_dir=dbsnp_dir,
+            set_pon=set_pon,
+            pon_vcf=pon_vcf,
+            cosmic_vcf=cosmic_vcf,
+            cosmic_dir=cosmic_dir,
+            tumor_name=sample_id + "_tumor",
+            normal_name=sample_id + "_normal",
+            docker=sentieon_docker,
+            sample=sample_id,
+            disk_size=disk_size,
+            cluster_config=cluster_config
+        }
+        
+        call annovar.annovar as TNscope_annovar {
+            input:
+            sample=sample_id,
+            vcf=TNscope.TNscope_vcf,
+            database=database,
+            docker=annovar_docker,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+        }
 
-		call vcf2maf.vcf2maf as TNscope_vcf2maf {
-			input:
-			sample=sample_id,
-			multianno_txt=TNscope_annovar.multianno_txt,
-			docker=maftools_docker,
-			cluster_config=cluster_config,
-			disk_size=disk_size
-		}
-	}
+        call vcf2maf.vcf2maf as TNscope_vcf2maf {
+            input:
+            sample=sample_id,
+            multianno_txt=TNscope_annovar.multianno_txt,
+            docker=maftools_docker,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+        }
+    }
 
-	if (varscan) {
-		call somatic.somatic as somatic {
-			input:
-			sample=sample_id,
-			tumor_bam=tumor_BQSR.recaled_bam,
-			tumor_bam_index=tumor_BQSR.recaled_bam_index,
-			normal_bam=normal_BQSR.recaled_bam,
-			normal_bam_index=normal_BQSR.recaled_bam_index,
-			ref_dir=ref_dir,
-			fasta=fasta,        
-			docker=varscan_docker,	
-			disk_size=disk_size,
-			cluster_config=cluster_config
-		}
+    if (varscan) {
+        call somatic.somatic as somatic {
+            input:
+            sample=sample_id,
+            tumor_bam=tumor_BQSR.recaled_bam,
+            tumor_bam_index=tumor_BQSR.recaled_bam_index,
+            normal_bam=normal_BQSR.recaled_bam,
+            normal_bam_index=normal_BQSR.recaled_bam_index,
+            ref_dir=ref_dir,
+            fasta=fasta,        
+            docker=varscan_docker,	
+            disk_size=disk_size,
+            cluster_config=cluster_config
+        }
 
-		call processSomatic.processSomatic as processSomatic {
-			input:
-			sample=sample_id,
-			varscan_snp=somatic.varscan_snp,
-			varscan_indel=somatic.varscan_indel,     
-			docker=varscan_docker,	
-			disk_size=disk_size,
-			cluster_config=cluster_config
-		}
+        call processSomatic.processSomatic as processSomatic {
+            input:
+            sample=sample_id,
+            varscan_snp=somatic.varscan_snp,
+            varscan_indel=somatic.varscan_indel,     
+            docker=varscan_docker,	
+            disk_size=disk_size,
+            cluster_config=cluster_config
+        }
 
-		call somaticFilter.somaticFilter as somaticFilter {
-			input:
-			sample=sample_id,
-			varscan_snp_somatic_hc=processSomatic.varscan_snp_somatic_hc,
-			varscan_snp_germline_hc=processSomatic.varscan_snp_germline_hc,
-			varscan_snp_loh_hc=processSomatic.varscan_snp_loh_hc,
-			varscan_indel_somatic_hc=processSomatic.varscan_indel_somatic_hc,
-			varscan_indel_germline_hc=processSomatic.varscan_indel_germline_hc,
-			varscan_indel_loh_hc=processSomatic.varscan_indel_loh_hc,
-			varscan_indel=somatic.varscan_indel,   
-			docker=varscan_docker,	
-			disk_size=disk_size,
-			cluster_config=cluster_config
-		}
+        call somaticFilter.somaticFilter as somaticFilter {
+            input:
+            sample=sample_id,
+            varscan_snp_somatic_hc=processSomatic.varscan_snp_somatic_hc,
+            varscan_snp_germline_hc=processSomatic.varscan_snp_germline_hc,
+            varscan_snp_loh_hc=processSomatic.varscan_snp_loh_hc,
+            varscan_indel_somatic_hc=processSomatic.varscan_indel_somatic_hc,
+            varscan_indel_germline_hc=processSomatic.varscan_indel_germline_hc,
+            varscan_indel_loh_hc=processSomatic.varscan_indel_loh_hc,
+            varscan_indel=somatic.varscan_indel,   
+            docker=varscan_docker,	
+            disk_size=disk_size,
+            cluster_config=cluster_config
+        }
 
-		call annovar.annovar as snp_somatic_annovar {
-			input: 
-			sample=sample_id,
-			vcf=somaticFilter.varscan_snp_somatic_filter,
-			database=database,
-			docker=annovar_docker,
-			cluster_config=cluster_config,
-			disk_size=disk_size
-		}
+        call annovar.annovar as snp_somatic_annovar {
+            input: 
+            sample=sample_id,
+            vcf=somaticFilter.varscan_snp_somatic_filter,
+            database=database,
+            docker=annovar_docker,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+        }
 
-		call vcf2maf.vcf2maf as snp_somatic_vcf2maf {
-			input:
-			sample=sample_id,
-			multianno_txt=snp_somatic_annovar.multianno_txt,
-			docker=maftools_docker,
-			cluster_config=cluster_config,
-			disk_size=disk_size
-		}
-		
-		call annovar.annovar as snp_loh_annovar {
-			input: 
-			sample=sample_id,
-			vcf=somaticFilter.varscan_snp_loh_filter,
-			database=database,
-			docker=annovar_docker,
-			cluster_config=cluster_config,
-			disk_size=disk_size
-		}
+        call vcf2maf.vcf2maf as snp_somatic_vcf2maf {
+            input:
+            sample=sample_id,
+            multianno_txt=snp_somatic_annovar.multianno_txt,
+            docker=maftools_docker,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+        }
+        
+        call annovar.annovar as snp_loh_annovar {
+            input: 
+            sample=sample_id,
+            vcf=somaticFilter.varscan_snp_loh_filter,
+            database=database,
+            docker=annovar_docker,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+        }
 
-		call vcf2maf.vcf2maf as snp_loh_vcf2maf {
-			input:
-			sample=sample_id,
-			multianno_txt=snp_loh_annovar.multianno_txt,
-			docker=maftools_docker,
-			cluster_config=cluster_config,
-			disk_size=disk_size
-		}
-		
-		call annovar.annovar as indel_somatic_annovar {
-			input: 
-			sample=sample_id,
-			vcf=somaticFilter.varscan_indel_somatic_filter,
-			database=database,
-			docker=annovar_docker,
-			cluster_config=cluster_config,
-			disk_size=disk_size
-		}
-		
-		call vcf2maf.vcf2maf as indel_somatic_vcf2maf {
-			input:
-			sample=sample_id,
-			multianno_txt=indel_somatic_annovar.multianno_txt,
-			docker=maftools_docker,
-			cluster_config=cluster_config,
-			disk_size=disk_size
-		}
-		
-		call annovar.annovar as indel_loh_annovar {
-			input: 
-			sample=sample_id,
-			vcf=somaticFilter.varscan_indel_loh_filter,
-			database=database,
-			docker=annovar_docker,
-			cluster_config=cluster_config,
-			disk_size=disk_size
-		}
+        call vcf2maf.vcf2maf as snp_loh_vcf2maf {
+            input:
+            sample=sample_id,
+            multianno_txt=snp_loh_annovar.multianno_txt,
+            docker=maftools_docker,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+        }
+        
+        call annovar.annovar as indel_somatic_annovar {
+            input: 
+            sample=sample_id,
+            vcf=somaticFilter.varscan_indel_somatic_filter,
+            database=database,
+            docker=annovar_docker,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+        }
+        
+        call vcf2maf.vcf2maf as indel_somatic_vcf2maf {
+            input:
+            sample=sample_id,
+            multianno_txt=indel_somatic_annovar.multianno_txt,
+            docker=maftools_docker,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+        }
+        
+        call annovar.annovar as indel_loh_annovar {
+            input: 
+            sample=sample_id,
+            vcf=somaticFilter.varscan_indel_loh_filter,
+            database=database,
+            docker=annovar_docker,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+        }
 
-		call vcf2maf.vcf2maf as indel_loh_vcf2maf {
-			input:
-			sample=sample_id,
-			multianno_txt=indel_loh_annovar.multianno_txt,
-			docker=maftools_docker,
-			cluster_config=cluster_config,
-			disk_size=disk_size
-		}
-	}
+        call vcf2maf.vcf2maf as indel_loh_vcf2maf {
+            input:
+            sample=sample_id,
+            multianno_txt=indel_loh_annovar.multianno_txt,
+            docker=maftools_docker,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+        }
+    }
 }