vcf to txt

tasks/replicate_consensus.wdl

@@ -6,8 +6,8 @@ task replicate_consensus {
 	String disk_size
 	
 	command <<<
-
-		python /opt/replicates_consensus.py -vcf ${chromo_file} -prefix ${chromo}
+		cat ${chromo_file} | grep -v '##' > ${chromo}.txt
+		python /opt/replicates_consensus.py -vcf ${chromo}.txt -prefix ${chromo}
 
 
 	>>>