vcf

tasks/benchmark.wdl

@@ -18,12 +18,10 @@ task benchmark {
 		cp -r ${benchmarking_dir} /cromwell_root/tmp/
 
 		gunzip ${vcf} -c > unzip.vcf
-
-		cat unzip.vcf | grep '##' | grep -v 'contig' | cat - ${contig} > header
 		cat unzip.vcf | grep '#CHROM' > name
 		cat unzip.vcf | grep -v '#' > body
 		cat body | grep -w '^chr1\|^chr2\|^chr3\|^chr4\|^chr5\|^chr6\|^chr7\|^chr8\|^chr9\|^chr10\|^chr11\|^chr12\|^chr13\|^chr14\|^chr15\|^chr16\|^chr17\|^chr18\|^chr19\|^chr20\|^chr21\|^chr22\|^chrX' > body.filtered
-		cat header name body.filtered > filtered.vcf
+		cat unzip.vcf | grep '##' | grep -v 'contig' | cat - ${contig} name body.filtered > filtered.vcf
 
  
 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip filtered.vcf -c > ${project}.${sample}.rtg.vcf.gz