rtg

tasks/benchmark.wdl

 	File vcf
 	File benchmarking_dir
 	File sdf
+	String project
 	String sample = basename(vcf,".raw.vcf.gz")
 	String fasta
 	String docker
 
 		gunzip ${vcf} -c > unzip.vcf
  
-		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip unzip.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 ${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
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip unzip.vcf -c > ${project}.${sample}.rtg.vcf.gz
+		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${project}.${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
 
 
 		if [[ ${sample} =~ "LCL5" ]];then
         fi		
 
 
-        cat ${sample}_SNV/summary.txt > ${sample}_SNV_precision_recall.txt
-        cat ${sample}_INDEL/summary.txt > ${sample}_INDEL_precision_recall.txt
+        cat ${sample}_SNV/summary.txt > ${project}.${sample}_SNV_precision_recall.txt
+        cat ${sample}_INDEL/summary.txt > ${project}.${sample}_INDEL_precision_recall.txt
         
 	>>>
 
 	}
 
 	output {
-		File rtg_vcf = "${sample}.rtg.vcf.gz"
-		File rtg_vcf_index = "${sample}.rtg.vcf.gz.tbi"
+		File rtg_vcf = "${project}.${sample}.rtg.vcf.gz"
+		File rtg_vcf_index = "${project}.${sample}.rtg.vcf.gz.tbi"
 		File SNV_result = "${sample}_SNV_precision_recall.txt"
 		File Indel_result = "${sample}_INDEL_precision_recall.txt"
 		File file_list = "files.txt"

workflow.wdl

 		vcf=LCL5,
 		benchmarking_dir=benchmarking_dir,
 		sdf=sdf,
+		project=project,
 		fasta=fasta,
 		docker=BENCHMARKdocker,
 		cluster_config=BIGcluster_config,
 		vcf=LCL6,
 		benchmarking_dir=benchmarking_dir,
 		sdf=sdf,
+		project=project,
 		fasta=fasta,
 		docker=BENCHMARKdocker,
 		cluster_config=BIGcluster_config,
 		vcf=LCL7,
 		benchmarking_dir=benchmarking_dir,
 		sdf=sdf,
+		project=project,
 		fasta=fasta,
 		docker=BENCHMARKdocker,
 		cluster_config=BIGcluster_config,
 		vcf=LCL8,
 		benchmarking_dir=benchmarking_dir,
 		sdf=sdf,
+		project=project,
 		fasta=fasta,
 		docker=BENCHMARKdocker,
 		cluster_config=BIGcluster_config,