name

tasks/filter_vcf.wdl

 		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 body.filtered > ${sample}.filtered.vcf
 		/opt/ccdg/bedtools-2.27.1/bin/bedtools intersect -a ${sample}.filtered.vcf -b ${bed} > body.bed.filtered
-		cat header body.bed.filtered > ${project}.chrom.bed.filtered.vcf
+		cat header body.bed.filtered > ${project}.${sample}.chrom.bed.filtered.vcf
 		/opt/ccdg/bedtools-2.27.1/bin/bedtools intersect -a ${benchmark_region} -b ${bed} > benchmark_region_query_bed.bed
 
 	>>>

tasks/sentieon.wdl

 		File is_metrics_header = "is_metrics.header"
 		File is_metrics_data = "${sample}.is_metrics"
 		File hs_metrics_header = "hs_metrics.header"
-		File hs_metrics_data = "${sample}.hs_metrics"		
+		File hs_metrics_data = "${sample}.hs_mtrics"		
 	}
 }