Use the HGREF

tasks/pre.wdl

@@ -20,10 +20,10 @@ task pre {
 
 		if [[ ${sample} =~ "LCL7"  ]]; then
 			/opt/hap.py/bin/pre.py ${vcf} ${sample}vcf.gz \
-				-r ${ref_dir}/${fasta} -D -L --fixchr --gender male --threads $nt --logfile ${sample}.normalization.log
+				-r ${HGREF} -D -L --fixchr --gender male --threads $nt --logfile ${sample}.normalization.log
 		else
 			/opt/hap.py/bin/pre.py ${vcf} ${sample}vcf.gz \
-				-r ${ref_dir}/${fasta} -D -L --fixchr --gender female --threads $nt --logfile ${sample}.normalization.log
+				-r ${HGREF} -D -L --fixchr --gender female --threads $nt --logfile ${sample}.normalization.log
 		fi
 
 	>>>