fix bug

tasks/picard.wdl

@@ -14,7 +14,8 @@ task picard {
 		set -o pipefail
 		set -e
 		nt=$(nproc)
-		java -jar /usr/bin/picard/picard.jar LiftoverVcf I=${vcf} O=${sample}_picard.vcf REJECT=rejected_variants.vcf CHAIN=${chain_dir}/${chain} R=${ref_dir}/${fasta}
+		#java -jar /usr/bin/picard/picard.jar LiftoverVcf I=${vcf} O=${sample}_picard.vcf REJECT=rejected_variants.vcf CHAIN=${chain_dir}/${chain} R=${ref_dir}/${fasta}
+		LiftoverVcf -I ${vcf} -O ${sample}_picard.vcf -REJECT rejected_variants.vcf -CHAIN ${chain_dir}/${chain} -R ${ref_dir}/${fasta}
 	>>>
 	
 	runtime {