benchmark dir

tasks/benchmark.wdl

 		nt=$(nproc)
 		mkdir -p /cromwell_root/tmp
 		cp -r ${ref_dir} /cromwell_root/tmp/
+		cp -r ${benchmarking_dir} /cromwell_root/tmp/
 
 		export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa
 
 		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.rtg.vcf.gz
 
 		if [[ ${sample} =~ "LCL5" ]];then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL5.high.confidence.calls.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL5.high.confidence.calls.vcf.gz ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 	    elif [[ ${sample} =~ "LCL6" ]]; then
-	    	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL6.high.confidence.calls.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+	    	/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL6.high.confidence.calls.vcf.gz ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
         elif [[ ${sample} =~ "LCL7" ]]; then
-        	/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL7.high.confidence.calls.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+        	/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL7.high.confidence.calls.vcf.gz ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 	    elif [[ ${sample} =~ "LCL8" ]]; then
-			/opt/hap.py/bin/hap.py ${benchmarking_dir}/LCL8.high.confidence.calls.vcf.gz ${sample}.rtg.vcf.gz -f ${benchmarking_dir}/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
+			/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL8.high.confidence.calls.vcf.gz ${sample}.rtg.vcf.gz -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
         else
         	echo "only for quartet samples"
         fi		
 
-        ls reference_datasets_v202103/ > files.txt
+        ls /cromwell_root/tmp/reference_datasets_v202103/ > files.txt
 	>>>
 
 	runtime {
 		File summary = "${sample}.summary.csv"
 		File extended = "${sample}.extended.csv"
 		File metrics = "${sample}.metrics.json.gz"
-		File file_list="files.txt"
+		File file_list = "files.txt"
 	}
 }