fix bug

defaults

     "vcf2maf_r_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/",
-    "regions": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/agilent_v6.bed",
-    "PONmode": true,
+    "regions": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/agilent_v6_cosmic_hg38.bed",
+    "set_pon": true,
     "cosmic_vcf": "CosmicCodingMuts.hg38.v91.vcf",
     "cosmic_dir": "oss://pgx-reference-data/reference/cosmic/",
     "disk_size": "200",

inputs

 {
+  "{{ project_name }}.fastq_1": "{{ fastq_1 }}",
+  "{{ project_name }}.fastq_2": "{{ fastq_2 }}",
+  "{{ project_name }}.normal_recaled_bam": "{{ normal_recaled_bam }}",
+  "{{ project_name }}.normal_recaled_bam_index": "{{ normal_recaled_bam_index }}",
+  "{{ project_name }}.type": "{{ type }}",
   "{{ project_name }}.fasta": "{{ fasta }}",
   "{{ project_name }}.ref_dir": "{{ ref_dir }}",
   "{{ project_name }}.dbsnp": "{{ dbsnp }}",
   "{{ project_name }}.sentieon_docker": "{{ sentieon_docker }}",
   "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",
   "{{ project_name }}.vcf2maf_r_docker": "{{ vcf2maf_r_docker }}",
-  "{{ project_name }}.bcftools_docker": "{{ bcftools_docker }}",
   "{{ project_name }}.database": "{{ database }}",
-  "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
   "{{ project_name }}.regions": "{{ regions }}",
-  "{{ project_name }}.PONmode": "{{ PONmode }}",
+  "{{ project_name }}.set_pon": "{{ set_pon }}",
+  "{{ project_name }}.pon_vcf": "{{ pon_vcf }}",
   "{{ project_name }}.cosmic_vcf": "{{ cosmic_vcf }}",
   "{{ project_name }}.cosmic_dir": "{{ cosmic_dir }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",

tasks/BQSR.wdl

 	File regions
 	String dbsnp
 	String db_mills
-	File realigned_bam1
-	File realigned_bam_index1
+	File realigned_bam
+	File realigned_bam_index
 	String docker
 	String cluster_config
 	String disk_size
 		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
 		nt=$(nproc)
 
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${realigned_bam1} --interval ${regions} --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${realigned_bam} --interval ${regions} --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table
 
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${realigned_bam1} -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 plot QualCal -o ${sample}_bqsrreport.pdf ${sample}_recal_data.csv
+		${SENTIEON_INSTALL_DIR}/bin/sentieon plot bqsr -o ${sample}_bqsrreport.pdf ${sample}_recal_data.csv
 
 	>>>
 

tasks/PON.wdl

 	String SENTIEON_INSTALL_DIR
 	String SENTIEON_LICENSE
 	String sample
-	Boolean PONmode
 
 	File ref_dir
 	String fasta
 		set -e
 		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
 		nt=$(nproc)
-		if [ ${PONmode} ]; then
-			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
-		else
-			touch ${sample}_pon.vcf
-		fi
+		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 {

tasks/TNscope.wdl

 	String cluster_config
 
 	String fasta
-	File corealigner_bam
-	File corealigner_bam_index
+	File? corealigner_bam
+	File? corealigner_bam_index
+	File tumor_recaled_bam
+	File tumor_recaled_bam_index
 	String dbsnp
 	String disk_size
 
-	Boolean PONmode
+	Boolean set_pon
 	String? cosmic_vcf
 	File? cosmic_dir
-	File panel_of_normal_vcf
+	File? pon_vcf
 	
+	String pon_command = if set_pon then "--pon /cromwell_root/tmp/PON/$(basename ${pon_vcf}) --cosmic /cromwell_root/tmp/PON/${cosmic_vcf}" else ""
+	String input_command = if defined(corealigner_bam) then "-i ${corealigner_bam} --tumor_sample ${tumor_name} --normal_sample ${normal_name}" else "-i ${tumor_recaled_bam} --tumor_sample ${tumor_name}"
 	
 	command <<<
 		set -o pipefail
 		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
 		nt=$(nproc)
 
-		if [ ${PONmode} ]; then
-			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}
-			PONcommand="--pon ${panel_of_normal_vcf} --cosmic /cromwell_root/tmp/cosmic/${cosmic_vcf}"
-		else
-			PONcommand=""
-		fi
-		
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${corealigner_bam} --algo TNscope --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} PONcommand ${sample}.TNscope.TN.vcf
+		mkdir -p /cromwell_root/tmp/PON/
+		cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/PON/
+		cp ${pon_vcf} /cromwell_root/tmp/PON/
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/${cosmic_vcf}
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/$(basename ${pon_vcf})
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} --algo TNscope ${input_command} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNscope.TN.vcf
 		
 	>>>
 

tasks/TNseq.wdl

 task TNseq {
 	File ref_dir
 	File dbsnp_dir
-	Array[String] sample
+	String sample
 	String SENTIEON_INSTALL_DIR
 	String SENTIEON_LICENSE
 	String tumor_name
 	String cluster_config
 
 	String fasta
-	Array[File] corealigner_bam
-	Array[File] corealigner_bam_index
+	File? corealigner_bam
+	File? corealigner_bam_index
+	File tumor_recaled_bam
+	File tumor_recaled_bam_index
 	String dbsnp
 	String disk_size
-	
-	Boolean PONmode
+
+	Boolean set_pon
 	String? cosmic_vcf
 	File? cosmic_dir
-	File panel_of_normal_vcf
-
+	File? pon_vcf
+	
+	String pon_command = if set_pon then "--pon /cromwell_root/tmp/PON/$(basename ${pon_vcf}) --cosmic /cromwell_root/tmp/PON/${cosmic_vcf}" else ""
+	String input_command = if defined(corealigner_bam) then "-i ${corealigner_bam} --tumor_sample ${tumor_name} --normal_sample ${normal_name}" else "-i ${tumor_recaled_bam} --tumor_sample ${tumor_name}"
 
 	command <<<
 		set -o pipefail
 		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
 		nt=$(nproc)
 
-		if [ ${PONmode} ]; then
-			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}
-			PONcommand="--pon ${panel_of_normal_vcf} --cosmic /cromwell_root/tmp/cosmic/${cosmic_vcf}"
-		else
-			PONcommand=""
-		fi
-		
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${sep=" -i " corealigner_bam} --algo TNhaplotyper --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} PONcommand ${sep=" " sample}.TNseq.TN.vcf
+		mkdir -p /cromwell_root/tmp/PON/
+		cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/PON/
+		cp ${pon_vcf} /cromwell_root/tmp/PON/
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/${cosmic_vcf}
+		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/$(basename ${pon_vcf})
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} --algo TNhaplotyper ${input_command} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNseq.TN.vcf
 
 	>>>
 
 	}
 
 	output {
-		File TNseq_vcf= "${sep=" " sample}.TNseq.TN.vcf"
-		File TNseq_vcf_index = "${sep=" " sample}.TNseq.TN.vcf.idx"
+		File TNseq_vcf= "${sample}.TNseq.TN.vcf"
+		File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx"
 	}
 
 }

tasks/bcftools.wdl

 	String docker
 	String cluster_config
 	String disk_size
-	Boolean PONmode
+	Boolean set_pon
 
 
 	command <<<
 		set -o pipefail
 		set -e
 		
-		if [ ${PONmode} ]; then
+		if [ ${set_pon} ]; then
 			mkdir -p /cromwell_root/tmp/bcftools/
 			for i in ${sep=" " pon_vcf}
 			do

tasks/corealigner.wdl

 	File dbsnp_dir
 	File dbmills_dir
 
-	Array[String] sample
+	String sample
 	String SENTIEON_INSTALL_DIR
 	String SENTIEON_LICENSE
 	String docker
 
 	String dbsnp
 	String db_mills
-	Array[File] tumor_recaled_bam
-	Array[File] tumor_recaled_bam_index
-	Array[File] normal_recaled_bam
-	Array[File] normal_recaled_bam_index
+	File tumor_recaled_bam
+	File tumor_recaled_bam_index
+	File normal_recaled_bam
+	File normal_recaled_bam_index
 	String disk_size
 
 
 		set -e
 		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
 		nt=$(nproc)
-		#${sep=" " tumor_recaled_bam}
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${sep=" -i " tumor_recaled_bam} -i ${sep=" -i " normal_recaled_bam} --algo Realigner -k ${dbmills_dir}/${db_mills} -k ${dbsnp_dir}/${dbsnp} ${sep=" " sample}_corealigned.bam				
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${tumor_recaled_bam} -i ${normal_recaled_bam} --algo Realigner -k ${dbmills_dir}/${db_mills} -k ${dbsnp_dir}/${dbsnp} ${sample}_corealigned.bam				
 	>>>
 	
 	runtime {
 	}
 
 	output {
-		File corealigner_bam = "${sep=" " sample}_corealigned.bam"
-		File corealigner_bam_index = "${sep=" " sample}_corealigned.bam.bai"
+		File corealigner_bam = "${sample}_corealigned.bam"
+		File corealigner_bam_index = "${sample}_corealigned.bam.bai"
 	}	
 }
 

workflow.wdl

 import "./tasks/deduped_Metrics.wdl" as deduped_Metrics
 import "./tasks/Realigner.wdl" as Realigner
 import "./tasks/BQSR.wdl" as BQSR
-#import "./tasks/corealigner.wdl" as corealigner
+import "./tasks/corealigner.wdl" as corealigner
 import "./tasks/PON.wdl" as PON
-import "./tasks/bcftools.wdl" as bcftools
-#import "./tasks/TNseq.wdl" as TNseq
-#import "./tasks/TNscope.wdl" as TNscope
-#import "./tasks/annovar.wdl" as annovar
-#import "./tasks/vcf2maf.wdl" as vcf2maf
+import "./tasks/TNseq.wdl" as TNseq
+import "./tasks/TNscope.wdl" as TNscope
+import "./tasks/annovar.wdl" as annovar
+import "./tasks/vcf2maf.wdl" as vcf2maf
 
 
 workflow {{ project_name }} {
 
-	File inputSamplesFile
-	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
-	#Array[String] sample
+	File fastq_1
+	File fastq_2
+	File? normal_recaled_bam
+	File? normal_recaled_bam_index
+	String type
 
 	String SENTIEON_INSTALL_DIR
 	String SENTIEON_LICENSE
 	String sentieon_docker
 	String annovar_docker
 	String vcf2maf_r_docker
-	String bcftools_docker
 	
 	File ref_dir
 	String fasta
 	File dbsnp_dir
 	String dbsnp
 	File regions
-	File database
 	String disk_size
 	String cluster_config
 
-	Boolean PONmode
+	Boolean set_pon
+	File? pon_vcf
 	File? cosmic_dir
 	String? cosmic_vcf
 
 	Boolean set_annovar
+	File? database
 	Boolean set_vcf2maf
-	
 
-	scatter (sample in inputSamples) {
-		call mapping.mapping as tumor_mapping {
-			input: 
-			group=sample[0] + "_tumor",
-			sample=sample[0] + "_tumor",
-			fastq_1=sample[1],
-			fastq_2=sample[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 mapping {
+		input: 
+		group=sample + '_' + type,
+		sample=sample + '_' + type,
+		fastq_1=fastq_1,
+		fastq_2=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[0] + "_tumor",
-			docker=sentieon_docker,
-			disk_size=disk_size,
-			cluster_config=cluster_config
-		}
+	call Metrics.Metrics as Metrics {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		SENTIEON_LICENSE=SENTIEON_LICENSE,
+		fasta=fasta,
+		ref_dir=ref_dir,
+		sorted_bam=mapping.sorted_bam,
+		sorted_bam_index=mapping.sorted_bam_index,
+		sample=sample + '_' + type,
+		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[0] + "_tumor",
-			docker=sentieon_docker,
-			disk_size=disk_size,
-			cluster_config=cluster_config
-		}
+	call Dedup.Dedup as Dedup {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		SENTIEON_LICENSE=SENTIEON_LICENSE,
+		sorted_bam=mapping.sorted_bam,
+		sorted_bam_index=mapping.sorted_bam_index,
+		sample=sample + '_' + type,
+		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[0] + "_tumor",
-			docker=sentieon_docker,
-			disk_size=disk_size,
-			cluster_config=cluster_config
-		}
+	call deduped_Metrics.deduped_Metrics as deduped_Metrics {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		SENTIEON_LICENSE=SENTIEON_LICENSE,
+		fasta=fasta,
+		ref_dir=ref_dir,
+		Dedup_bam=Dedup.Dedup_bam,
+		Dedup_bam_index=Dedup.Dedup_bam_index,
+		sample=sample + '_' + type,
+		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[0] + "_tumor",
-			docker=sentieon_docker,
-			disk_size=disk_size,
-			regions=regions,
-			cluster_config=cluster_config
-		}
+	call Realigner.Realigner as Realigner {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		SENTIEON_LICENSE=SENTIEON_LICENSE,
+		fasta=fasta,
+		ref_dir=ref_dir,
+		Dedup_bam=Dedup.Dedup_bam,
+		Dedup_bam_index=Dedup.Dedup_bam_index,
+		db_mills=db_mills,
+		dbmills_dir=dbmills_dir,
+		sample=sample + '_' + type,
+		docker=sentieon_docker,
+		disk_size=disk_size,
+		regions=regions,
+		cluster_config=cluster_config
+	}
+
+	call BQSR.BQSR as BQSR {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		SENTIEON_LICENSE=SENTIEON_LICENSE,
+		fasta=fasta,
+		ref_dir=ref_dir,
+		realigned_bam=Realigner.realigner_bam,
+		realigned_bam_index=Realigner.realigner_bam_index,
+		db_mills=db_mills,
+		dbmills_dir=dbmills_dir,
+		dbsnp=dbsnp,
+		dbsnp_dir=dbsnp_dir,
+		sample=sample + '_' + type,
+		regions=regions,
+		docker=sentieon_docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
 
-		call BQSR.BQSR as tumor_BQSR {
+	if (set_pon && type == "normal") {
+		call PON.PON as PON {
 			input:
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
+			sample=sample,
 			fasta=fasta,
 			ref_dir=ref_dir,
-			realigned_bam1=tumor_Realigner.realigner_bam,
-			realigned_bam_index1=tumor_Realigner.realigner_bam_index,
-			db_mills=db_mills,
-			dbmills_dir=dbmills_dir,
+			normal_recaled_bam=BQSR.recaled_bam,
+			normal_recaled_bam_index=BQSR.recaled_bam_index,
+			cosmic_vcf=cosmic_vcf,
+			cosmic_dir=cosmic_dir,
 			dbsnp=dbsnp,
 			dbsnp_dir=dbsnp_dir,
-			sample=sample[0] + "_tumor",
-			regions=regions,
 			docker=sentieon_docker,
 			disk_size=disk_size,
 			cluster_config=cluster_config
 		}
 	}
-
-	scatter (sample in inputSamples) {	
-		call mapping.mapping as normal_mapping {
-			input: 
-			group=sample[0] + "_normal",
-			sample=sample[0] + "_normal",
-			fastq_1=sample[3],
-			fastq_2=sample[4],
-			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[0] + "_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[0] + "_normal",
-			docker=sentieon_docker,
-			disk_size=disk_size,
-			cluster_config=cluster_config
-		}
-
-		call deduped_Metrics.deduped_Metrics as normal_deduped_Metrics {
+	
+	if (type == "tumor" && defined(normal_recaled_bam)) {
+		call corealigner.corealigner as corealigner {
 			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[0] + "_normal",
+			sample=sample,
 			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[0] + "_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_bam1=normal_Realigner.realigner_bam,
-			realigned_bam_index1=normal_Realigner.realigner_bam_index,
 			db_mills=db_mills,
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
 			dbsnp_dir=dbsnp_dir,
-			sample=sample[0] + "_normal",
-			regions=regions,
-			docker=sentieon_docker,
-			disk_size=disk_size,
-			cluster_config=cluster_config
-		}
-
-		call PON.PON as PON {
-			input:
-			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			sample=sample[0],
-			PONmode=PONmode,
-			fasta=fasta,
-			ref_dir=ref_dir,
-			normal_recaled_bam=normal_BQSR.recaled_bam,
-			normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
-			cosmic_vcf=cosmic_vcf,
-			cosmic_dir=cosmic_dir,
-			dbsnp=dbsnp,
-			dbsnp_dir=dbsnp_dir,
-			docker=sentieon_docker,
+			tumor_recaled_bam=BQSR.recaled_bam,
+			tumor_recaled_bam_index=BQSR.recaled_bam_index,
+			normal_recaled_bam=normal_recaled_bam,
+			normal_recaled_bam_index=normal_recaled_bam_index,
 			disk_size=disk_size,
 			cluster_config=cluster_config
 		}
+		File bam_to_use = corealigner.corealigner_bam
 	}
 
-	call bcftools.bcftools as bcftools {
+	if (type == "tumor" && !defined(normal_recaled_bam)) {
+		File bam_to_use = BQSR.recaled_bam
+	}	
+
+	#File bam_to_use = select_first([corealigner.corealigner_bam, BQSR.recaled_bam])
+
+
+	call TNseq.TNseq as TNseq {
 		input:
-		PONmode=PONmode,
-		pon_vcf=PON.pon_vcf,
-		docker=bcftools_docker,
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		SENTIEON_LICENSE=SENTIEON_LICENSE,
+		fasta=fasta,
+		ref_dir=ref_dir,
+		corealigner_bam=corealigner.corealigner_bam,
+		corealigner_bam_index=corealigner.corealigner_bam_index,
+		tumor_recaled_bam=BQSR.recaled_bam,
+		tumor_recaled_bam_index=BQSR.recaled_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 + "_tumor",
+		normal_name=sample + "_normal",
+		docker=sentieon_docker,
+		sample=sample,
 		disk_size=disk_size,
 		cluster_config=cluster_config
 	}
-	
-}
+    
+	call TNscope.TNscope as TNscope {
+		input:
+		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+		SENTIEON_LICENSE=SENTIEON_LICENSE,
+		fasta=fasta,
+		ref_dir=ref_dir,
+		corealigner_bam=corealigner.corealigner_bam,
+		corealigner_bam_index=corealigner.corealigner_bam_index,
+		tumor_recaled_bam=BQSR.recaled_bam,
+		tumor_recaled_bam_index=BQSR.recaled_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 + "_tumor",
+		normal_name=sample + "_normal",
+		docker=sentieon_docker,
+		sample=sample,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+    
+	if (set_annovar && defined(TNscope.TNscope_vcf) && defined(TNseq.TNseq_vcf)){
+        call annovar.annovar as annovar {
+            input:
+            docker=annovar_docker,
+            database=database,
+            tnscope_vcf_file=TNscope.TNscope_vcf,
+            tnseq_vcf_file=TNseq.TNseq_vcf,
+            sample=sample,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+        }
+
+    	if (set_vcf2maf){
+        	call vcf2maf.vcf2maf as vcf2maf {
+            	input:
+    	        docker=vcf2maf_r_docker,
+        	    multianno_tnscope_txt=annovar.multianno_tnscope_txt,
+            	multianno_tnseq_txt=annovar.multianno_tnseq_txt,
+    	        sample=sample,
+    	        cluster_config=cluster_config,
+    	        disk_size=disk_size
+    	    }
+		}
+    }
+}