test regions

tasks/Haplotyper.wdl

@@ -15,13 +15,14 @@ task Haplotyper {
 
 	File? regions
 	Int? interval_padding
-	String INTERVAL = if regions then "--interval ${regions} --interval_padding ${interval_padding}" else ""
+	String 
 
 command <<<
 		set -o pipefail
 		set -e
 		export SENTIEON_LICENSE=192.168.0.55:8990
-		nt=$(nproc)	
+		nt=$(nproc)
+		if ${regions} then INTERVAL="--interval ${regions} --interval_padding ${interval_padding}" else INTERVAL=""
 		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt \
 		-i ${recaled_bam} ${INTERVAL} \
 		--algo Haplotyper -d ${dbsnp_dir}/${dbsnp} ${sample}_hc.vcf