test

tasks/PON.wdl

@@ -10,6 +10,7 @@ task PON {
 	String cosmic_vcf
 	File dbsnp_dir
 	String dbsnp
+	File regions
 
 	File normal_recaled_bam
 	File normal_recaled_bam_index
@@ -25,7 +26,7 @@ task PON {
 		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
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -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 {

workflow.wdl

@@ -11,6 +11,7 @@ workflow {{ project_name }} {
 	String cosmic_vcf
 	File dbsnp_dir
 	String dbsnp
+	File regions
 
 	File normal_recaled_bam
 	File normal_recaled_bam_index
@@ -25,6 +26,7 @@ workflow {{ project_name }} {
 		sample=sample_id,
 		fasta=fasta,
 		ref_dir=ref_dir,
+		regions=regions,
 		normal_recaled_bam=normal_recaled_bam,
 		normal_recaled_bam_index=normal_recaled_bam_index,
 		cosmic_vcf=cosmic_vcf,