add parameter: interval

tasks/TNscope.wdl

@@ -2,8 +2,8 @@ task TNscope {
 
 	File ref_dir
 	File dbsnp_dir
+	File regions
 	String sample
-
 	String SENTIEON_INSTALL_DIR
 	String SENTIEON_LICENSE
 	String tumor_name
@@ -43,9 +43,9 @@ task TNscope {
 		fi
 
 		if ${TN}; then
-			${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} ${pon_command} ${sample}.TNscope.TN.vcf
+			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${corealigner_bam} --algo TNscope --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNscope.TN.vcf
 		else
-			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${tumor_recaled_bam} --algo TNscope --tumor_sample ${tumor_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNscope.TN.vcf
+			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${tumor_recaled_bam} --algo TNscope --tumor_sample ${tumor_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNscope.TN.vcf
 		fi
 		
 	>>>

tasks/TNseq.wdl

@@ -1,6 +1,7 @@
 task TNseq {
 	File ref_dir
 	File dbsnp_dir
+	File regions
 	String sample
 	String SENTIEON_INSTALL_DIR
 	String SENTIEON_LICENSE
@@ -40,9 +41,9 @@ task TNseq {
 		fi
 
 		if ${TN}; then
-			${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} ${pon_command} ${sample}.TNseq.TN.vcf
+			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${corealigner_bam} --algo TNhaplotyper --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNseq.TN.vcf
 		else
-			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${tumor_recaled_bam} --algo TNhaplotyper --tumor_sample ${tumor_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNseq.TN.vcf
+			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${tumor_recaled_bam} --algo TNhaplotyper --tumor_sample ${tumor_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNseq.TN.vcf
 		fi
 	>>>
 

tasks/annovar.wdl

@@ -25,11 +25,11 @@ task annovar {
 	}
 
 	output {
-		File avinput_TNscope = "${sample}_TNscope.avinput"
-		File multianno_TNscope_txt = "${sample}_TNscope.hg38_multianno.txt"
-		File multianno_TNscope_vcf = "${sample}_TNscope.hg38_multianno.vcf"
-		File avinput_TNseq = "${sample}_TNseq.avinput"
-		File multianno_TNseq_txt = "${sample}_TNseq.hg38_multianno.txt"
-		File multianno_TNseq_vcf = "${sample}_TNseq.hg38_multianno.vcf"
+		File avinput_TNscope = "${sample}.TNscope.avinput"
+		File multianno_TNscope_txt = "${sample}.TNscope.hg38_multianno.txt"
+		File multianno_TNscope_vcf = "${sample}.TNscope.hg38_multianno.vcf"
+		File avinput_TNseq = "${sample}.TNseq.avinput"
+		File multianno_TNseq_txt = "${sample}.TNseq.hg38_multianno.txt"
+		File multianno_TNseq_vcf = "${sample}.TNseq.hg38_multianno.vcf"
 	}
 }

tasks/vcf2maf.wdl

@@ -8,8 +8,10 @@ task vcf2maf {
 	String disk_size
 
 	command <<<
-		vcf2maf ${multianno_TNscope_txt} ${sample}_TNscope.MAF
-		vcf2maf ${multianno_TNseq_txt} ${sample}_TNseq.MAF
+		vcf2maf ${multianno_TNscope_txt} ${sample}.TNscope.MAF
+		vcf2maf ${multianno_TNseq_txt} ${sample}.TNseq.MAF
+		awk -F '\t' '{if(($1=="Tumor_Sample_Barcode")||($1~"^${sample}" && $180=="PASS")){print $0}}' ${sample}.TNscope.MAF > ${sample}.TNscope.PASS.MAF
+		awk -F '\t' '{if(($1=="Tumor_Sample_Barcode")||($1~"^${sample}" && $180=="PASS")){print $0}}' ${sample}.TNseq.MAF > ${sample}.TNseq.PASS.MAF
 	>>>
 
 	runtime {
@@ -20,7 +22,9 @@ task vcf2maf {
 	}
 
 	output {
-		File tnscope_maf = "${sample}_TNscope.MAF"
-		File tnseq_maf = "${sample}_TNseq.MAF"
+		File tnscope_maf = "${sample}.TNscope.MAF"
+		File tnseq_maf = "${sample}.TNseq.MAF"
+		File tnscope_pass_maf = "${sample}.TNscope.PASS.MAF"
+		File tnseq_pass_maf = "${sample}.TNseq.PASS.MAF"
 	}
 }

workflow.wdl

@@ -211,6 +211,7 @@ workflow {{ project_name }} {
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
 			fasta=fasta,
 			ref_dir=ref_dir,
+			regions=regions,
 			corealigner_bam=corealigner.corealigner_bam,
 			corealigner_bam_index=corealigner.corealigner_bam_index,
 			tumor_recaled_bam=BQSR.recaled_bam,
@@ -236,6 +237,7 @@ workflow {{ project_name }} {
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
 			fasta=fasta,
 			ref_dir=ref_dir,
+			regions=regions,
 			corealigner_bam=corealigner.corealigner_bam,
 			corealigner_bam_index=corealigner.corealigner_bam_index,
 			tumor_recaled_bam=BQSR.recaled_bam,