test regions

tasks/Haplotyper.wdl

@@ -21,7 +21,13 @@ task Haplotyper {
 		set -e
 		export SENTIEON_LICENSE=192.168.0.55:8990
 		nt=$(nproc)
-		if ${regions} then INTERVAL="--interval ${regions} --interval_padding ${interval_padding}" else INTERVAL=""
+		
+		if [ ${regions} ]; then
+		  INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
+		else
+		  INTERVAL=""
+		fi
+
 		${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