Test

README.md

@@ -0,0 +1,53 @@
+### Variant Calling
+This APP developed for somatic short variant discovery (SNVs + Indels).
+
+***Supported callers***
+* TNseq (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+* TNhaplotyper (This caller is only available in `v0.1.0` as it is too outdated)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.
+
+***Accepted data***
+* TN matched WES
+* TN matched WGS
+
+The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs).
+
+### New Releases
+* The TNhaplotyper, named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2.
+* The `corealigner` step has been removed.
+* The `vcf2maf` step has been removed. Thus, the final output is the annotated `VCF`.
+
+### Getting Started
+
+We recommend using choppy system and Aliyun OSS service. The command will look like this:
+
+```
+# Activate the choppy environment
+$ open-choppy-env
+
+# Install the APP
+$ choppy install YaqingLiu/variant-calling-latest [-f]
+
+# List the parameters
+$ choppy samples YaqingLiu/variant-calling-latest [--no-default]
+
+# Submit you task with the `samples.csv file` and `project name`
+$ choppy batch YaqingLiu/variant-calling-latest samples.csv -p Project [-l project: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.
+
+The parameters that must need contains: sample_id,normal_fastq_1,normal_fastq_2,tumor_fastq_1,tumor_fastq_2
+
+
+**Please carefully check**
+* the reference genome
+* bed file
+* the caller you want to use
+* whether PoN needs to be set

defaults

@@ -0,0 +1,28 @@
+{
+    "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",
+    "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
+}

inputs

@@ -1,17 +1,34 @@
 {
-  "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
-  "{{ project_name }}.ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
-  "{{ project_name }}.dbsnp": "dbsnp_146.hg38.vcf",
-  "{{ project_name }}.recaled_bam": "{{ recaled_bam }}",
-  "{{ project_name }}.SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
-  "{{ project_name }}.db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
-  "{{ project_name }}.cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
-  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2020.10.07",
-  "{{ project_name }}.dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
-  "{{ project_name }}.sample": "{{ sample_id }}",
-  "{{ project_name }}.disk_size": "500", 
-  "{{ project_name }}.recaled_bam_index": "{{ recaled_bam_index }}",
-  "{{ project_name }}.regions": "oss://pgx-reference-data/bed/cbcga/S07604514_Covered.bed",
-  "{{ project_name }}.interval_padding": "0"
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.tumor_bam": "{{ tumor_bam }}",
+  "{{ project_name }}.tumor_bai": "{{ tumor_bai }}",
+  "{{ project_name }}.tumor_table": "{{ tumor_table }}",
+  "{{ project_name }}.normal_bam": "{{ normal_bam }}",
+  "{{ project_name }}.normal_bai": "{{ normal_bai }}",
+  "{{ project_name }}.normal_table": "{{ normal_table }}",
+  "{{ project_name }}.fasta": "{{ fasta }}",
+  "{{ project_name }}.ref_dir": "{{ ref_dir }}",
+  "{{ project_name }}.dbsnp": "{{ dbsnp }}",
+  "{{ project_name }}.dbsnp_dir": "{{ dbsnp_dir }}",
+  "{{ project_name }}.SENTIEON_INSTALL_DIR": "{{ SENTIEON_INSTALL_DIR }}",
+  "{{ 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 }}",
+  "{{ 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 }}.tnseq": {{ tnseq | tojson }},
+  "{{ project_name }}.tnscope": {{ tnscope | tojson }},
+  "{{ project_name }}.varscan": {{ varscan | tojson }}
 }
-

tasks/BQSR.wdl

@@ -1,48 +0,0 @@
-task BQSR {
-	
-    File ref_dir
-    File dbsnp_dir
-    File dbmills_dir
-	String sample
-	String SENTIEON_INSTALL_DIR
-	String fasta
-	String dbsnp
-	String db_mills
-	File realigned_bam
-	File realigned_bam_index
-	String docker
-	String cluster_config
-	String disk_size
-
-	
-	command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=192.168.0.55:8990
-		nt=$(nproc)
-
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${realigned_bam} --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table
-
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${realigned_bam} -q ${sample}_recal_data.table --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table.post --algo ReadWriter ${sample}.sorted.deduped.realigned.recaled.bam
-
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --algo QualCal --plot --before ${sample}_recal_data.table --after ${sample}_recal_data.table.post ${sample}_recal_data.csv
-
-		${SENTIEON_INSTALL_DIR}/bin/sentieon plot QualCal -o ${sample}_bqsrreport.pdf ${sample}_recal_data.csv
-
-	>>>
-	runtime {
-		docker:docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"	
-	}
-
-	output {
-		File recal_table = "${sample}_recal_data.table"
-		File recal_post = "${sample}_recal_data.table.post"
-		File recaled_bam = "${sample}.sorted.deduped.realigned.recaled.bam"
-		File recaled_bam_index = "${sample}.sorted.deduped.realigned.recaled.bam.bai"
-		File recal_csv = "${sample}_recal_data.csv"
-		File bqsrreport_pdf = "${sample}_bqsrreport.pdf"
-	}
-}

tasks/Dedup.wdl

@@ -1,40 +0,0 @@
-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

@@ -1,49 +0,0 @@
-task Haplotyper {
-	
-    File ref_dir
-    File dbsnp_dir
-
-	String SENTIEON_INSTALL_DIR
-	String fasta
-	File recaled_bam
-	File recaled_bam_index
-	String dbsnp
-	String sample
-	String docker
-	String cluster_config
-	String disk_size
-
-	File? regions
-	Int? interval_padding
-	
-	command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=192.168.0.55:8990
-		nt=$(nproc)
-
-		if [ ${regions} ]; then
-		  INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
-		else
-		  INTERVAL=""
-		fi
-
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt \
-		-i ${recaled_bam} $INTERVAL \
-		--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

@@ -1,56 +0,0 @@
-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

@@ -1,41 +0,0 @@
-task Realigner {
-
-    File ref_dir
-    File dbmills_dir
-
-	String SENTIEON_INSTALL_DIR
-	String sample
-	String fasta
-
-	File Dedup_bam
-	File Dedup_bam_index
-	String db_mills
-	String docker	
-	String cluster_config
-	String disk_size
-
-
-	command <<<
-	set -o pipefail
-	set -e
-	export SENTIEON_LICENSE=192.168.0.55:8990
-	nt=$(nproc)
-	${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} --algo Realigner -k ${dbmills_dir}/${db_mills} ${sample}.sorted.deduped.realigned.bam
-	
-	>>>
-
-	runtime {
-		docker:docker
-		cluster: cluster_config
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File realigner_bam = "${sample}.sorted.deduped.realigned.bam"
-		File realigner_bam_index = "${sample}.sorted.deduped.realigned.bam.bai"
-
-	}
-}
-
-

tasks/TNscope.wdl

@@ -1,42 +1,69 @@
 task TNscope {
+  
+  String sample
+  String SENTIEON_INSTALL_DIR
+  String SENTIEON_LICENSE
+  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
+  String tumor_name
+  String normal_name
 
-	File ref_dir
-    File dbsnp_dir
+  File ref_dir
+  String fasta
+  File dbsnp_dir
+  String dbsnp
+  File? regions
+  Int? interval_padding
+  File? pon_vcf
+
+  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 ${regions} --interval_padding ${interval_padding}"
+    else
+      INTERVAL=""
+    fi
+
+    if [ ${pon_vcf} ]; then
+      PON="--pon ${pon_vcf}"
+      ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${pon_vcf}
+    else
+      PON=""
+    fi
     
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
+    -r ${ref_dir}/${fasta} $INTERVAL \
+    -i ${tumor_recaled_bam} -q ${tumor_recal_table} \
+    -i ${normal_recaled_bam} -q ${normal_recal_table} \
+    --algo TNscope \
+    --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
+    --dbsnp ${dbsnp_dir}/${dbsnp} \
+    $PON \
+    ${sample}.TNscope.TN.vcf
+  >>>
+
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
 
-	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 = "${sample}.TNscope.TN.vcf.idx"
-	}
+  output {
+    File TNscope_vcf= "${sample}.TNscope.TN.vcf"
+    File TNscope_vcf_index = "${sample}.TNscope.TN.vcf.idx"
+  }
 
 }

tasks/TNseq.wdl

@@ -1,43 +1,89 @@
 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"
-	}
-
-}
 
+  String sample
+  String SENTIEON_INSTALL_DIR
+  String SENTIEON_LICENSE
+  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
+  String tumor_name
+  String normal_name
 
+  File ref_dir
+  String fasta
+  File germline_resource
+  File? regions
+  Int? interval_padding
+  File? pon_vcf
+
+  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 ${regions} --interval_padding ${interval_padding}"
+    else
+      INTERVAL=""
+    fi
+
+    if [ ${pon_vcf} ]; then
+      PON="--pon ${pon_vcf}"
+      ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${pon_vcf}
+    else
+      PON=""
+    fi
+
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
+    -r ${ref_dir}/${fasta} $INTERVAL \
+    -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 \
+    ${sample}.TNseq.TN.tmp.vcf \
+    --algo OrientationBias --tumor_sample ${tumor_name} \
+    ${sample}.orientation \
+    --algo ContaminationModel \
+    --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
+    --vcf ${germline_resource} \
+    --tumor_segments ${sample}.contamination.segments \
+    ${sample}.contamination
+    
+    sentieon driver -r REFERENCE \
+    --algo TNfilter \
+    --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
+    -v ${sample}.TNseq.TN.tmp.vcf \
+    --contamination ${sample}.contamination \
+    --tumor_segments ${sample}.contamination.segments \
+    --orientation_priors ${sample}.orientation \
+    ${sample}.TNseq.TN.vcf
+  >>>
+
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+
+  output {
+    File TNseq_vcf = "${sample}.TNseq.TN.vcf"
+    File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx"
+    File contamination = "${sample}.contamination"
+    File contamination_segments = "${sample}.contamination.segments"
+    File orientation = "${sample}.orientation"
+  }
+
+}

tasks/corealigner.wdl

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

@@ -1,37 +0,0 @@
-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

@@ -1,34 +0,0 @@
-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

@@ -1,39 +1,98 @@
-import "./tasks/Haplotyper.wdl" as Haplotyper
-
+import "./tasks/TNseq.wdl" as TNseq
+import "./tasks/TNscope.wdl" as TNscope
 
 workflow {{ project_name }} {
+    
+    String sample_id
+    File tumor_bam
+    File tumor_bai
+    File tumor_table
+    File normal_bam
+    File normal_bai
+    File normal_table
+
+    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
+    Int? interval_padding
+
+    File database
+    String disk_size
+    String cluster_config
 
-	File recaled_bam
-	File recaled_bam_index
+    File? tnseq_pon
+    File? tnscope_pon
+    File? cosmic_dir
+    String? cosmic_vcf
 
-	String SENTIEON_INSTALL_DIR
-	String sample
-	String docker
-	
-	String fasta
-	File ref_dir
-	File dbsnp_dir
-	String dbsnp
-	String disk_size
-	String cluster_config
+    Boolean germline
+    Boolean tnseq
+    Boolean tnscope
+    Boolean varscan
 
-	File? regions
-	Int? interval_padding
+    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_bam,
+            normal_recaled_bam_index=normal_bai,
+            normal_recal_table=normal_table,
+            tumor_recaled_bam=tumor_bam,
+            tumor_recaled_bam_index=tumor_bai,
+            tumor_recal_table=tumor_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,
+            pon_vcf=tnseq_pon,
+            docker=sentieon_docker,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+        }
+    }
 
-	call Haplotyper.Haplotyper as Haplotyper {
-		input:
-		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-		fasta=fasta,
-		ref_dir=ref_dir,
-		regions=regions,
-		interval_padding=interval_padding,
-		recaled_bam=recaled_bam,
-		recaled_bam_index=recaled_bam_index,
-		dbsnp=dbsnp,
-		dbsnp_dir=dbsnp_dir,
-		sample=sample,
-		docker=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_bam,
+            normal_recaled_bam_index=normal_bai,
+            normal_recal_table=normal_table,
+            tumor_recaled_bam=tumor_bam,
+            tumor_recaled_bam_index=tumor_bai,
+            tumor_recal_table=tumor_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
+        }
+    }
+}