fix bug

tasks/BQSR.wdl

@@ -1,52 +0,0 @@
-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_bam1
-	File realigned_bam_index1
-	String docker
-	String cluster_config
-	String disk_size
-
-	
-	command <<<
-		set -o pipefail
-		set -e
-		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_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 -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

@@ -1,43 +0,0 @@
-task Dedup {
-
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	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=${SENTIEON_LICENSE}
-		nt=$(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

@@ -1,39 +0,0 @@
-task Haplotyper {
-	
-	File ref_dir
-	File dbsnp_dir
-	
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	String fasta
-	File recaled_bam
-	File recaled_bam_index
-	File regions
-	String dbsnp
-	String sample
-	String docker
-	String cluster_config
-	String disk_size
-
-	command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-		nt=$(nproc)	
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver --interval ${regions} -r ${ref_dir}/${fasta} -t $nt -i ${recaled_bam} --algo Haplotyper -d ${dbsnp_dir}/${dbsnp} ${sample}_hc.vcf
-	>>>
-	
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File vcf = "${sample}_hc.vcf"
-		File vcf_idx = "${sample}_hc.vcf.idx"
-	}
-}
-
-

tasks/Metrics.wdl

@@ -1,57 +0,0 @@
-task Metrics {
-
-
-	File ref_dir
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	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=${SENTIEON_LICENSE}
-		nt=$(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/PON.wdl

@@ -1,46 +0,0 @@
-task PON {
-
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	String sample
-	Boolean PONmode
-
-	File ref_dir
-	String fasta
-	File cosmic_dir
-	String cosmic_vcf
-	File dbsnp_dir
-	String dbsnp
-
-	File normal_recaled_bam
-	File normal_recaled_bam_index
-	String docker
-	String cluster_config
-	String disk_size
-	
-	command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-		nt=$(nproc)
-		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 ${sample}_pon.vcf
-		fi
-	>>>
-	
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"	
-	}
-
-	output {
-		File pon_vcf = "${sample}_pon.vcf"
-	}
-}

tasks/Realigner.wdl

@@ -1,42 +0,0 @@
-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)
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} --algo Realigner -k ${dbmills_dir}/${db_mills} --interval_list ${regions} ${sample}.sorted.deduped.realigned.bam
-	>>>
-
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File realigner_bam = "${sample}.sorted.deduped.realigned.bam"
-		File realigner_bam_index = "${sample}.sorted.deduped.realigned.bam.bai"
-
-	}
-}
-
-

tasks/TNscope.wdl

@@ -1,57 +0,0 @@
-task TNscope {
-
-	File ref_dir
-	File dbsnp_dir
-	String sample
-
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	String tumor_name
-	String normal_name
-	String docker
-	String cluster_config
-
-	String fasta
-	File corealigner_bam
-	File corealigner_bam_index
-	String dbsnp
-	String disk_size
-
-	Boolean PONmode
-	String? cosmic_vcf
-	File? cosmic_dir
-	File? panel_of_normal_vcf
-	
-	
-	command <<<
-		set -o pipefail
-		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}
-			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 ${sample}.TNscope.TN.vcf
-		
-	>>>
-
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File TNscope_vcf= "${sample}.TNscope.TN.vcf"
-		File TNscope_vcf_index = "${sample}.TNscope.TN.vcf.idx"
-	}
-
-}

tasks/TNseq.wdl

@@ -1,57 +0,0 @@
-task TNseq {
-	File ref_dir
-	File dbsnp_dir
-	String sample
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	String tumor_name
-	String normal_name
-	String docker
-	String cluster_config
-
-	String fasta
-	File corealigner_bam
-	File corealigner_bam_index
-	String dbsnp
-	String disk_size
-	
-	Boolean PONmode
-	String? cosmic_vcf
-	File? cosmic_dir
-	File? panel_of_normal_vcf
-
-
-	command <<<
-		set -o pipefail
-		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}
-			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 TNhaplotyper --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} PONcommand ${sample}.TNseq.TN.vcf
-
-	>>>
-
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File TNseq_vcf= "${sample}.TNseq.TN.vcf"
-		File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx"
-	}
-
-}
-
-

tasks/annovar.wdl

@@ -1,35 +0,0 @@
-task annovar {
-
-	File tnscope_vcf_file
-	File tnseq_vcf_file
-	File database
-	String sample
-	String docker
-	String cluster_config
-	String disk_size
-
-
-	command <<<
-		set -o pipefail
-		set -e
-		nt=$(nproc)
-		/installations/annovar/table_annovar.pl ${tnscope_vcf_file} ${database} -buildver hg19 -out ${sample}_tnscope -remove -protocol refGene,cytoBand,genomicSuperDups,snp138,ljb26_all,cosmic78,clinvar_20170130,popfreq_all_20150413,intervar_20170202 -operation g,r,r,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
-		/installations/annovar/table_annovar.pl ${tnseq_vcf_file} ${database} -buildver hg19 -out ${sample}_tnseq -remove -protocol refGene,cytoBand,genomicSuperDups,snp138,ljb26_all,cosmic78,clinvar_20170130,popfreq_all_20150413,intervar_20170202 -operation g,r,r,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
-	>>>
-	
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File avinput_tnscope = "${sample}_tnscope.avinput"
-		File multianno_tnscope_txt = "${sample}_tnscope.hg19_multianno.txt"
-		File multianno_tnscope_vcf = "${sample}_tnscope.hg19_multianno.vcf"
-		File avinput_tnseq = "${sample}_tnseq.avinput"
-		File multianno_tnseq_txt = "${sample}_tnseq.hg19_multianno.txt"
-		File multianno_tnseq_vcf = "${sample}_tnseq.hg19_multianno.vcf"
-	}
-}

tasks/bcftools.wdl

@@ -1,21 +1,24 @@
 task bcftools {
 
-	#File pon_vcf1
-	#File pon_vcf2
-	#File pon_vcf3
-	File bcfpon
+	Array[File] bcfpon
 	String docker
 	String cluster_config
 	String disk_size
-	Boolean PONmode
-
 
 	command <<<
 		set -o pipefail
 		set -e
-		
-		if [ ${PONmode} ]; then
-			bcftools view ${bcfpon} -Oz -o $(basename ${bcfpon}.gz)
+
+		mkdir -p /cromwell_root/tmp/bcftools
+
+		for i in ${sep=" " bcfpon}
+		do
+		  bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$(basename $i.gz)
+		  bcftools index /cromwell_root/tmp/bcftools/$(basename $i.gz) -f
+		done
+
+		cd /cromwell_root/tmp/bcftools
+		bcftools merge -m all -f PASS,. --force-samples *.gz | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf
 			#mkdir -p /cromwell_root/tmp/bcftools
 			#bcftools view ${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/$(basename ${pon_vcf1}.gz)
 			#bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/$(basename ${pon_vcf1}.gz)
@@ -24,12 +27,13 @@ task bcftools {
 			#bcftools view ${pon_vcf1} -Oz -o $(basename ${pon_vcf1}.gz)
 			#bcftools view ${pon_vcf2} -Oz -o $(basename ${pon_vcf2}.gz)
 			#bcftools view ${pon_vcf2} -Oz -o $(basename ${pon_vcf3}.gz)
+
 			#for i in `ls *.gz`; do bcftools index $i -f; done
 			#bcftools merge -m all -f PASS,. --force-samples *.vcf.gz | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf
-		else
-			echo 1
+		#else
+		#	echo 1
 			#touch panel_of_normal.vcf
-		fi
+		#fi
 	>>>
 
 	runtime {

tasks/corealigner.wdl

@@ -1,46 +0,0 @@
-task corealigner {
-	
-	File ref_dir
-	File dbsnp_dir
-	File dbmills_dir
-
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	String docker
-	String cluster_config
-	String fasta
-	String sample
-
-	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=${SENTIEON_LICENSE}
-		nt=$(nproc)
-		#${sep=" " tumor_recaled_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} ${sample}_corealigned.bam				
-	>>>
-	
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File corealigner_bam = "${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 SENTIEON_LICENSE
-	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=${SENTIEON_LICENSE}
-		nt=$(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

@@ -1,35 +0,0 @@
-task mapping {
-
-	File ref_dir
-	String fasta
-	File fastq_1
-	File fastq_2
-
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	String group
-	String sample
-	String pl
-	String docker
-	String cluster_config
-	String disk_size
-
-	command <<<
-		set -o pipefail
-		set -e	
-		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-		nt=$(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"
-	}
-}

tasks/vcf2maf.wdl

@@ -1,26 +0,0 @@
-task vcf2maf {
-
-	File? multianno_tnscope_txt
-	File? multianno_tnseq_txt
-	String sample
-	String docker
-	String cluster_config
-	String disk_size
-
-	command <<<
-		vcf2maf ${multianno_tnscope_txt} ${sample}_tnscope.MAF
-		vcf2maf ${multianno_tnseq_txt} ${sample}_tnseq.MAF
-	>>>
-
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File tnscope_maf = "${sample}_tnscope.MAF"
-		File tnseq_maf = "${sample}_tnseq.MAF"
-	}
-}

workflow.wdl

@@ -1,56 +1,17 @@
-
-import "./tasks/corealigner.wdl" as corealigner
-import "./tasks/bcftools1.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/bcftools.wdl" as bcftools
 
 workflow {{ project_name }} {
-
-	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 dbmills_dir
-	String db_mills
-	File dbsnp_dir
-	String dbsnp
-	File regions
-	File database
+	String bcftools_docker
 	String disk_size
 	String cluster_config
-
-	Boolean PONmode
-	File? cosmic_dir
-	String? cosmic_vcf
-
-	Boolean set_annovar
-	Boolean set_vcf2maf
-
-
-	#File pon_vcf1
-	#File pon_vcf2
-	#File pon_vcf3
 	Array[File] BCF
 
-	scatter (sample in BCF) {
-		call bcftools.bcftools as bcftools {
-			input:
-			PONmode=PONmode,
-			bcfpon=sample,
-			#pon_vcf1=pon_vcf1,
-			#pon_vcf2=pon_vcf2,
-			#pon_vcf3=pon_vcf3,
-			docker=bcftools_docker,
-			disk_size=disk_size,
-			cluster_config=cluster_config
-		}
+	call bcftools.bcftools as bcftools {
+		input:
+		bcfpon=BCF,
+		docker=bcftools_docker,
+		disk_size=disk_size,
+		cluster_config=cluster_config
 	}
 }