Update: README.md

README.md

 
 **All callers are not activated by default**, which means the default setting is `false`. 
 You need to manually set the caller to `true` in the submitted sample.csv.
+The fields corresponding to these callers include `haplotyper`, `tnseq`, `tnscope`, `varscan`.
 
 **Germline**
 * Haplotyper
 
-If you only want to call germline variants, please set `germline` to true.
+If you only want to call germline variants, please set `haplotyper` to true.
 
 **Somatic**
 * TNseq (TNhaplotyper2)
 Variant caller can be selected by setting `ture/false` in the submitted sample.csv.
 
 ***Accepted data***
-* TN matched WES
-* TN matched WGS
+* TN matched WES for somatic variant calling
+* TN matched WGS for somatic variant calling
+* Normal-only WES for germline variant calling
+* Normal-only WGS for germline variant calling
 
 The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs).
 

defaults

 {
-    "fasta": "GRCh38.d1.vd1.fa",
-    "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
-    "dbsnp": "dbsnp_146.hg38.vcf",
-    "dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
-    "SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
-    "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",
-    "germline_resource_tbi": "oss://pgx-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz.tbi",
-    "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",
-    "maftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/r-base:4.0.2",
-    "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
-    "database": "oss://pgx-reference-data/annovar_hg38/",
-    "regions": "oss://pgx-reference-data/bed/cbcga/S07604514_Covered.bed",
-    "tnseq_pon": "",
-    "tnscope_pon": "",
-    "cosmic_vcf": "CosmicCodingMuts.hg38.v91.vcf",
-    "cosmic_dir": "oss://pgx-reference-data/reference/cosmic/",
-    "disk_size": "200",
-    "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
-    "germline": false,
-    "tnseq": true,
-    "tnscope": true,
-    "varscan": true
+  "tumor_fastq_1": "",
+  "tumor_fastq_2": "",
+  "fasta": "GRCh38.d1.vd1.fa",
+  "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+  "dbsnp": "dbsnp_146.hg38.vcf",
+  "dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+  "SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
+  "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",
+  "germline_resource_tbi": "oss://pgx-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz.tbi",
+  "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",
+  "database": "oss://pgx-reference-data/annovar_hg38/",
+  "regions": "oss://pgx-reference-data/bed/cbcga/S07604514_Covered.bed",
+  "tnseq_pon": "",
+  "tnscope_pon": "",
+  "disk_size": "200",
+  "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
+  "haplotyper": false,
+  "tnseq": false,
+  "tnscope": false,
+  "varscan": false
 }

inputs

   "{{ project_name }}.sentieon_docker": "{{ sentieon_docker }}",
   "{{ project_name }}.varscan_docker": "{{ varscan_docker }}",
   "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",
-  "{{ project_name }}.maftools_docker": "{{ maftools_docker }}",
   "{{ project_name }}.database": "{{ database }}",
   "{{ project_name }}.regions": "{{ regions }}",
   "{{ project_name }}.tnseq_pon": "{{ tnseq_pon }}",
   "{{ project_name }}.tnscope_pon": "{{ tnscope_pon }}",
-  "{{ project_name }}.cosmic_vcf": "{{ cosmic_vcf }}",
-  "{{ project_name }}.cosmic_dir": "{{ cosmic_dir }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}",
-  "{{ project_name }}.germline": {{ germline | tojson }},
+  "{{ project_name }}.haplotyper": {{ haplotyper | tojson }},
   "{{ project_name }}.tnseq": {{ tnseq | tojson }},
   "{{ project_name }}.tnscope": {{ tnscope | tojson }},
   "{{ project_name }}.varscan": {{ varscan | tojson }}

tasks/BQSR.wdl

 task BQSR {
-	
-	File ref_dir
-	File dbsnp_dir
-	File dbmills_dir
-	
-	String sample
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	String fasta
-	File? regions
-	String dbsnp
-	String db_mills
-	File realigned_bam
-	File realigned_bam_index
-	String docker
-	String cluster_config
-	String disk_size
+  
+  File ref_dir
+  File dbsnp_dir
+  File dbmills_dir
+  
+  String sample
+  String SENTIEON_INSTALL_DIR
+  String SENTIEON_LICENSE
+  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=${SENTIEON_LICENSE}
-		nt=$(nproc)
-		if [ ${regions} != "" ]; then
-			${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
-		else
-			${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} ${sample}_recal_data.table
-		fi
+  
+  command <<<
+    set -o pipefail
+    set -e
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+    if [ ${regions} != "" ]; then
+      ${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
+    else
+      ${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
+    fi
 
-		${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 -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 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 bqsr -o ${sample}_bqsrreport.pdf ${sample}_recal_data.csv
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon plot bqsr -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/"	
-	}
+  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"
-	}
+  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/Realigner.wdl

 task Realigner {
 
-	File ref_dir
-	File dbmills_dir
-
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	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=${SENTIEON_LICENSE}
-		nt=$(nproc)
-		
-		if [ ${regions} ]; then
-		  INTERVAL="--interval_list ${regions}"
-		else
-		  INTERVAL=""
-		fi
-		
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
-		-r ${ref_dir}/${fasta} $INTERVAL \
-		-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 = "${sample}.sorted.deduped.realigned.bam.bai"
-
-	}
+  File ref_dir
+  File dbmills_dir
+
+  String SENTIEON_INSTALL_DIR
+  String SENTIEON_LICENSE
+  String sample
+  String fasta
+
+  File? regions
+  File Dedup_bam
+  File Dedup_bam_index
+  String db_mills
+  String docker
+  String cluster_config
+  String disk_size
+  
+  command <<<
+    set -o pipefail
+    set -e
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+    
+    if [ ${regions} ]; then
+      INTERVAL="--interval_list ${regions}"
+    else
+      INTERVAL=""
+    fi
+    
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
+    -r ${ref_dir}/${fasta} $INTERVAL \
+    -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/annovar.wdl

 task annovar {
 
-	String sample
-	File vcf
-	String annotated_vcf = basename(vcf,".vcf")
-	File database
-	String docker
-	String cluster_config
-	String disk_size
+  String sample
+  File vcf
+  String annotated_vcf = basename(vcf,".vcf")
+  File database
+  String docker
+  String cluster_config
+  String disk_size
 
 
-	command <<<
-		set -o pipefail
-		set -e
-		nt=$(nproc)
-		/installations/annovar/table_annovar.pl ${vcf} ${database} -buildver hg38 -out ${annotated_vcf} -remove -protocol refGene,ensGene,knownGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,g,g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
-	>>>
-	
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    /installations/annovar/table_annovar.pl ${vcf} ${database} -buildver hg38 -out ${annotated_vcf} -remove -protocol refGene,ensGene,knownGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,g,g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
 
-	output {
-		File avinput = "${annotated_vcf}.avinput"
-		File multianno_txt = "${annotated_vcf}.hg38_multianno.txt"
-		File multianno = "${annotated_vcf}.hg38_multianno.vcf"
-	}
+  output {
+    File avinput = "${annotated_vcf}.avinput"
+    File multianno_txt = "${annotated_vcf}.hg38_multianno.txt"
+    File multianno = "${annotated_vcf}.hg38_multianno.vcf"
+  }
 }

tasks/processSomatic.wdl

 task processSomatic {
-    
-    String sample
-    File varscan_snp
-    File varscan_indel
-    
-    String docker
-    String cluster_config
-    String disk_size
+  
+  String sample
+  File varscan_snp
+  File varscan_indel
+  
+  String docker
+  String cluster_config
+  String disk_size
 
-    command <<<
-        cp ${varscan_snp} ./
-        cp ${varscan_indel} ./
-        java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.SNP.vcf
-        java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.INDEL.vcf
+  command <<<
+    cp ${varscan_snp} ./
+    cp ${varscan_indel} ./
+    java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.SNP.vcf
+    java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.INDEL.vcf
 
-    >>>
+  >>>
 
-    runtime {
-        docker: docker
-        cluster: cluster_config
-        systemDisk: "cloud_ssd 40"
-        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-    }
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
 
-    output {
-        File varscan_snp_somatic = "${sample}.VarScan.TN.SNP.Somatic.vcf"
-        File varscan_snp_germline = "${sample}.VarScan.TN.SNP.Germline.vcf"
-        File varscan_snp_loh = "${sample}.VarScan.TN.SNP.LOH.vcf"
-        File varscan_snp_somatic_hc = "${sample}.VarScan.TN.SNP.Somatic.hc.vcf"
-        File varscan_snp_germline_hc = "${sample}.VarScan.TN.SNP.Germline.hc.vcf"
-        File varscan_snp_loh_hc = "${sample}.VarScan.TN.SNP.LOH.hc.vcf"
-        File varscan_indel_somatic = "${sample}.VarScan.TN.INDEL.Somatic.vcf"
-        File varscan_indel_germline = "${sample}.VarScan.TN.INDEL.Germline.vcf"
-        File varscan_indel_loh = "${sample}.VarScan.TN.INDEL.LOH.vcf"
-        File varscan_indel_somatic_hc = "${sample}.VarScan.TN.INDEL.Somatic.hc.vcf"
-        File varscan_indel_germline_hc = "${sample}.VarScan.TN.INDEL.Germline.hc.vcf"
-        File varscan_indel_loh_hc = "${sample}.VarScan.TN.INDEL.LOH.hc.vcf"
-    }
+  output {
+    File varscan_snp_somatic = "${sample}.VarScan.TN.SNP.Somatic.vcf"
+    File varscan_snp_germline = "${sample}.VarScan.TN.SNP.Germline.vcf"
+    File varscan_snp_loh = "${sample}.VarScan.TN.SNP.LOH.vcf"
+    File varscan_snp_somatic_hc = "${sample}.VarScan.TN.SNP.Somatic.hc.vcf"
+    File varscan_snp_germline_hc = "${sample}.VarScan.TN.SNP.Germline.hc.vcf"
+    File varscan_snp_loh_hc = "${sample}.VarScan.TN.SNP.LOH.hc.vcf"
+    File varscan_indel_somatic = "${sample}.VarScan.TN.INDEL.Somatic.vcf"
+    File varscan_indel_germline = "${sample}.VarScan.TN.INDEL.Germline.vcf"
+    File varscan_indel_loh = "${sample}.VarScan.TN.INDEL.LOH.vcf"
+    File varscan_indel_somatic_hc = "${sample}.VarScan.TN.INDEL.Somatic.hc.vcf"
+    File varscan_indel_germline_hc = "${sample}.VarScan.TN.INDEL.Germline.hc.vcf"
+    File varscan_indel_loh_hc = "${sample}.VarScan.TN.INDEL.LOH.hc.vcf"
+  }
 }

tasks/somatic.wdl

 task somatic {
 
-    String sample
-    File normal_bam
-    File normal_bam_index
-    File tumor_bam
-    File tumor_bam_index
+  String sample
+  File normal_bam
+  File normal_bam_index
+  File tumor_bam
+  File tumor_bam_index
 
-    File ref_dir
-    String fasta    
-    String docker
-    String cluster_config
-    String disk_size
+  File ref_dir
+  String fasta  
+  String docker
+  String cluster_config
+  String disk_size
 
-    command <<<
-        samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somatic --mpileup 1 --min-coverage 3 --min-coverage-normal 3 --min-coverage-tumor 3 --min-var-freq 0.08 --p-value 0.10 --somatic-p-value 0.05 --output-vcf 1 --output-snp ${sample}.VarScan.TN.SNP --output-indel ${sample}.VarScan.TN.INDEL --strand-filter 1
-    >>>
+  command <<<
+    samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somatic --mpileup 1 --min-coverage 3 --min-coverage-normal 3 --min-coverage-tumor 3 --min-var-freq 0.08 --p-value 0.10 --somatic-p-value 0.05 --output-vcf 1 --output-snp ${sample}.VarScan.TN.SNP --output-indel ${sample}.VarScan.TN.INDEL --strand-filter 1
+  >>>
 
-    runtime {
-        docker: docker
-        cluster: cluster_config
-        systemDisk: "cloud_ssd 40"
-        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-    }
-    output {
-        File varscan_snp = "${sample}.VarScan.TN.SNP.vcf"
-        File varscan_indel = "${sample}.VarScan.TN.INDEL.vcf"
-        
-    }
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  output {
+    File varscan_snp = "${sample}.VarScan.TN.SNP.vcf"
+    File varscan_indel = "${sample}.VarScan.TN.INDEL.vcf"
+    
+  }
 }

tasks/somaticFilter.wdl

 task somaticFilter {
-    
-    String sample
-    File varscan_snp_somatic_hc
-    File varscan_snp_germline_hc
-    File varscan_snp_loh_hc
-    File varscan_indel_somatic_hc
-    File varscan_indel_germline_hc
-    File varscan_indel_loh_hc
-    File varscan_indel
+  
+  String sample
+  File varscan_snp_somatic_hc
+  File varscan_snp_germline_hc
+  File varscan_snp_loh_hc
+  File varscan_indel_somatic_hc
+  File varscan_indel_germline_hc
+  File varscan_indel_loh_hc
+  File varscan_indel
 
-    String docker
-    String cluster_config
-    String disk_size
+  String docker
+  String cluster_config
+  String disk_size
 
-    command <<<
-        java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.Somatic.filter.vcf
+  command <<<
+    java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.Somatic.filter.vcf
 
-        java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.Germline.filter.vcf
+    java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.Germline.filter.vcf
 
-        java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.LOH.filter.vcf
+    java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.TN.SNP.LOH.filter.vcf
 
-        java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.Somatic.filter.vcf
+    java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.Somatic.filter.vcf
 
-        java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.Germline.filter.vcf
+    java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.Germline.filter.vcf
 
-        java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.LOH.filter.vcf
-    >>>
+    java -Xmx12g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.TN.INDEL.LOH.filter.vcf
+  >>>
 
-    runtime {
-        docker: docker
-        cluster: cluster_config
-        systemDisk: "cloud_ssd 40"
-        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-    }
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
 
-    output {
+  output {
 		File varscan_snp_somatic_filter = "${sample}.VarScan.TN.SNP.Somatic.filter.vcf"
-        File varscan_snp_germline_filter = "${sample}.VarScan.TN.SNP.Germline.filter.vcf"
+    File varscan_snp_germline_filter = "${sample}.VarScan.TN.SNP.Germline.filter.vcf"
 		File varscan_snp_loh_filter = "${sample}.VarScan.TN.SNP.LOH.filter.vcf"
 		File varscan_indel_somatic_filter = "${sample}.VarScan.TN.INDEL.Somatic.filter.vcf"
-        File varscan_indel_germline_filter = "${sample}.VarScan.TN.INDEL.Germline.filter.vcf"
+    File varscan_indel_germline_filter = "${sample}.VarScan.TN.INDEL.Germline.filter.vcf"
 		File varscan_indel_loh_filter = "${sample}.VarScan.TN.INDEL.LOH.filter.vcf"
-    }
+  }
 }

workflow.wdl

 
 
 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 germline_resource
-    File germline_resource_tbi
-    
-    File? regions
-    Int? interval_padding
+  String SENTIEON_INSTALL_DIR
+  String SENTIEON_LICENSE
+  String sentieon_docker
+  String varscan_docker
+  String annovar_docker
 
-    File database
-    String disk_size
-    String cluster_config
+  File ref_dir
+  String fasta
+  File dbmills_dir
+  String db_mills
+  File dbsnp_dir
+  String dbsnp
+  File germline_resource
+  File germline_resource_tbi
+  
+  File? regions
+  Int? interval_padding
 
-    File? tnseq_pon
-    File? tnscope_pon
-    File? cosmic_dir
-    String? cosmic_vcf
+  File database
+  String disk_size
+  String cluster_config
 
-    Boolean germline
-    Boolean tnseq
-    Boolean tnscope
-    Boolean varscan
-    
+  File? tnseq_pon
+  File? tnscope_pon
+
+  Boolean haplotyper
+  Boolean tnseq
+  Boolean tnscope
+  Boolean varscan
+
+  if (tumor_fastq_1 != "") {
     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
+      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
+      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
+      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
+      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
+      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
+      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',
-        regions=regions,
-        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',
+    regions=regions,
+    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',
-        regions=regions,
-        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',
+    regions=regions,
+    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
+  }
+
+  if (haplotyper) {
+    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,
+      recaled_table=normal_BQSR.recal_table,
+      dbsnp=dbsnp,
+      dbsnp_dir=dbsnp_dir,
+      regions=regions,
+      docker=sentieon_docker,
+      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,
+      sample=sample_id,
+      normal_recaled_bam=normal_BQSR.recaled_bam,
+      normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
+      normal_recal_table=normal_BQSR.recal_table,
+      tumor_recaled_bam=tumor_BQSR.recaled_bam,
+      tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
+      tumor_recal_table=tumor_BQSR.recal_table,
+      normal_name=sample_id + "_normal",
+      tumor_name=sample_id + "_tumor",
+      fasta=fasta,
+      ref_dir=ref_dir,
+      regions=regions,
+      interval_padding=interval_padding,
+      germline_resource=germline_resource,
+      germline_resource_tbi=germline_resource_tbi,
+      pon_vcf=tnseq_pon,
+      docker=sentieon_docker,
+      cluster_config=cluster_config,
+      disk_size=disk_size
     }
 
-    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 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
     }
+  }
 
-    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,
-            recaled_table=normal_BQSR.recal_table,
-            dbsnp=dbsnp,
-            dbsnp_dir=dbsnp_dir,
-            regions=regions,
-            docker=sentieon_docker,
-            disk_size=disk_size,
-            cluster_config=cluster_config
-        }
+  if (tnscope) {
+    call TNscope.TNscope as TNscope {
+      input:
+      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+      SENTIEON_LICENSE=SENTIEON_LICENSE,
+      sample=sample_id,
+      normal_recaled_bam=normal_BQSR.recaled_bam,
+      normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
+      normal_recal_table=normal_BQSR.recal_table,
+      tumor_recaled_bam=tumor_BQSR.recaled_bam,
+      tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
+      tumor_recal_table=tumor_BQSR.recal_table,
+      normal_name=sample_id + "_normal",
+      tumor_name=sample_id + "_tumor",
+      fasta=fasta,
+      ref_dir=ref_dir,
+      regions=regions,
+      interval_padding=interval_padding,
+      dbsnp=dbsnp,
+      dbsnp_dir=dbsnp_dir,
+      pon_vcf=tnscope_pon,
+      docker=sentieon_docker,
+      cluster_config=cluster_config,
+      disk_size=disk_size
     }
     
-    if (tnseq) {
-        call TNseq.TNseq as TNseq {
-            input:
-            SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-            SENTIEON_LICENSE=SENTIEON_LICENSE,
-            sample=sample_id,
-            normal_recaled_bam=normal_BQSR.recaled_bam,
-            normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
-            normal_recal_table=normal_BQSR.recal_table,
-            tumor_recaled_bam=tumor_BQSR.recaled_bam,
-            tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
-            tumor_recal_table=tumor_BQSR.recal_table,
-            normal_name=sample_id + "_normal",
-            tumor_name=sample_id + "_tumor",
-            fasta=fasta,
-            ref_dir=ref_dir,
-            regions=regions,
-            interval_padding=interval_padding,
-            germline_resource=germline_resource,
-            germline_resource_tbi=germline_resource_tbi,
-            pon_vcf=tnseq_pon,
-            docker=sentieon_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 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,
-            sample=sample_id,
-            normal_recaled_bam=normal_BQSR.recaled_bam,
-            normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
-            normal_recal_table=normal_BQSR.recal_table,
-            tumor_recaled_bam=tumor_BQSR.recaled_bam,
-            tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
-            tumor_recal_table=tumor_BQSR.recal_table,
-            normal_name=sample_id + "_normal",
-            tumor_name=sample_id + "_tumor",
-            fasta=fasta,
-            ref_dir=ref_dir,
-            regions=regions,
-            interval_padding=interval_padding,
-            dbsnp=dbsnp,
-            dbsnp_dir=dbsnp_dir,
-            pon_vcf=tnscope_pon,
-            docker=sentieon_docker,
-            cluster_config=cluster_config,
-            disk_size=disk_size
-        }
-        
-        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 (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 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 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_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 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 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
+    }
     }
+  }
 }