fix bug

tasks/picard.wdl

@@ -14,7 +14,7 @@ task picard {
 		set -o pipefail
 		set -e
 		nt=$(nproc)
-		java -jar /usr/bin/picard/picard.jar LiftoverVcf I = ${vcf} O = ${sample}_picard.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}
 	>>>
 	
 	runtime {
@@ -26,5 +26,6 @@ task picard {
 
 	output {
 		File picard_vcf = "${sample}_picard.vcf"
+		File rejected_variants = "rejected_variants.vcf"
 	}
 }