rtg name

tasks/benchmark.wdl

@@ -30,8 +30,8 @@ task benchmark {
 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip filtered.vcf -c > ${sample}.rtg.vcf.gz
 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.rtg.vcf.gz
 
-		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${project}.${sample}.rtg.vcf.gz -o ${sample}.rtg.SNV.vcf.gz --snps-only
-		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${project}.${sample}.rtg.vcf.gz -o ${sample}.rtg.INDEL.vcf.gz --non-snps-only
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${sample}.rtg.vcf.gz -o ${sample}.rtg.SNV.vcf.gz --snps-only
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${sample}.rtg.vcf.gz -o ${sample}.rtg.INDEL.vcf.gz --non-snps-only
 
 		if [[ ${sample} =~ "LCL5" ]];then
 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b /cromwell_root/tmp/reference_datasets_v202103/LCL5.high.confidence.calls.SNV.vcf.gz -c ${sample}.rtg.SNV.vcf.gz -o ${sample}_SNV -t ${sdf} --evaluation-regions=/cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed
@@ -49,8 +49,8 @@ task benchmark {
         	echo "only for quartet samples"
         fi		
 
-        cat ${sample}_SNV/summary.txt > ${project}.${sample}_SNV_precision_recall.txt
-        cat ${sample}_INDEL/summary.txt > ${project}.${sample}_INDEL_precision_recall.txt
+        cat ${sample}_SNV/summary.txt > ${project}_SNV_precision_recall.txt
+        cat ${sample}_INDEL/summary.txt > ${project}_INDEL_precision_recall.txt
 
 	>>>
 
@@ -64,7 +64,7 @@ task benchmark {
 	output {
 		File rtg_vcf = "${project}.${sample}.rtg.vcf.gz"
 		File rtg_vcf_index = "${project}.${sample}.rtg.vcf.gz.tbi"
-		File SNV_result = "${project}.${sample}_SNV_precision_recall.txt"
-		File Indel_result = "${project}.${sample}_INDEL_precision_recall.txt"
+		File SNV_result = "${project}_SNV_precision_recall.txt"
+		File Indel_result = "${project}_INDEL_precision_recall.txt"
 	}
 }