test regions

tasks/Haplotyper.wdl

@@ -1,6 +1,5 @@
 task Haplotyper {
 	
-	
     File ref_dir
     File dbsnp_dir
 
@@ -14,12 +13,16 @@ task Haplotyper {
 	String cluster_config
 	String disk_size
 
+	File? regions
+
 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 ${recaled_bam} --algo Haplotyper -d ${dbsnp_dir}/${dbsnp} ${sample}_hc.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt \
+		-i ${recaled_bam} --interval ${regions} \
+		--algo Haplotyper -d ${dbsnp_dir}/${dbsnp} ${sample}_hc.vcf
 	>>>
 	
 	runtime {

workflow.wdl

@@ -19,11 +19,14 @@ workflow {{ project_name }} {
 	String disk_size
 	String cluster_config
 
+	File? regions
+
 	call Haplotyper.Haplotyper as Haplotyper {
 		input:
 		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 		fasta=fasta,
 		ref_dir=ref_dir,
+		regions=regions,
 		recaled_bam=recaled_bam,
 		recaled_bam_index=recaled_bam_index,
 		dbsnp=dbsnp,