rename vcf

tasks/benchmark.wdl

@@ -42,28 +42,32 @@ task benchmark {
 			cat filtered.vcf | grep '##' > header
 			cat filtered.vcf | grep -v '#' > body
 			cat header LCL5_name body > LCL5.vcf
-			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip LCL5.vcf -c > ${project}.${sample}.rtg.vcf.gz
+			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip LCL5.vcf -c > ${project}.${sample}.reformed.vcf.gz
+			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${project}.${sample}.reformed.vcf.gz
 	    elif [[ ${sample} =~ "LCL6" ]]; then
 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b /cromwell_root/tmp/reference_datasets_v202103/LCL6.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
 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b /cromwell_root/tmp/reference_datasets_v202103/LCL6.high.confidence.calls.INDEL.vcf.gz -c ${sample}.rtg.INDEL.vcf.gz -o ${sample}_INDEL -t ${sdf} --evaluation-regions=/cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed
 			cat filtered.vcf | grep '##' > header
 			cat filtered.vcf | grep -v '#' > body
 			cat header LCL6_name body > LCL6.vcf
-			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip LCL6.vcf -c > ${project}.${sample}.rtg.vcf.gz
+			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip LCL6.vcf -c > ${project}.${sample}.reformed.vcf.gz
+			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${project}.${sample}.reformed.vcf.gz
         elif [[ ${sample} =~ "LCL7" ]]; then
 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b /cromwell_root/tmp/reference_datasets_v202103/LCL7.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
 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b /cromwell_root/tmp/reference_datasets_v202103/LCL7.high.confidence.calls.INDEL.vcf.gz -c ${sample}.rtg.INDEL.vcf.gz -o ${sample}_INDEL -t ${sdf} --evaluation-regions=/cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed
 			cat filtered.vcf | grep '##' > header
 			cat filtered.vcf | grep -v '#' > body
 			cat header LCL7_name body > LCL7.vcf
-			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip LCL7.vcf -c > ${project}.${sample}.rtg.vcf.gz
+			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip LCL7.vcf -c > ${project}.${sample}.reformed.vcf.gz
+			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${project}.${sample}.reformed.vcf.gz
 	    elif [[ ${sample} =~ "LCL8" ]]; then
 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b /cromwell_root/tmp/reference_datasets_v202103/LCL8.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
 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfeval -b /cromwell_root/tmp/reference_datasets_v202103/LCL8.high.confidence.calls.INDEL.vcf.gz -c ${sample}.rtg.INDEL.vcf.gz -o ${sample}_INDEL -t ${sdf} --evaluation-regions=/cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed
 			cat filtered.vcf | grep '##' > header
 			cat filtered.vcf | grep -v '#' > body
 			cat header LCL8_name body > LCL8.vcf
-			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip LCL8.vcf -c > ${project}.${sample}.rtg.vcf.gz
+			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip LCL8.vcf -c > ${project}.${sample}.reformed.vcf.gz
+			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${project}.${sample}.reformed.vcf.gz
         else
         	echo "only for quartet samples"
         fi		
@@ -82,8 +86,8 @@ task benchmark {
 	}
 
 	output {
-		File rtg_vcf = "${project}.${sample}.rtg.vcf.gz"
-		File rtg_vcf_index = "${project}.${sample}.rtg.vcf.gz.tbi"
+		File rtg_vcf = "${project}.${sample}.reformed.vcf.gz"
+		File rtg_vcf_index = "${project}.${sample}.reformed.vcf.gz.tbi"
 		File SNV_result = "${project}.${sample}_SNV_precision_recall.txt"
 		File Indel_result = "${project}.${sample}_INDEL_precision_recall.txt"
 	}