0/0

tasks/benchmark.wdl

@@ -21,7 +21,8 @@ task benchmark {
 		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 unzip.vcf | grep '##' | grep -v 'contig' | cat - ${contig} name body.filtered > filtered.vcf
+		cat body.filtered | grep -v '0/0' > body.filtered.gt
+		cat unzip.vcf | grep '##' | grep -v 'contig' | cat - ${contig} name body.filtered.gt > filtered.vcf
 
 		echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL5" > LCL5_name
 		echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL6" > LCL6_name

workflow.wdl

@@ -89,7 +89,7 @@ workflow {{ project_name }} {
 		LCL8_vcf_idx=LCL8benchmark.rtg_vcf,
 		project=project,
 		docker=BENCHMARKdocker,
-		cluster_config=SMALLcluster_config,
+		cluster_config=BIGcluster_config,
 		disk_size=disk_size,
 	}