benchmark

tasks/benchmark.wdl

@@ -26,28 +26,28 @@ task benchmark {
 		echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL8" > LCL8_name
 
 
-		if [[ ${sample} =~ "D5" ]];then
+		if [[ ${sample} =~ "LCL5" ]];then
 			/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL5.high.confidence.calls.vcf ${filtered_vcf} -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 			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 > ${sample}.reformed.vcf.gz
 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.reformed.vcf.gz
-		elif [[ ${sample} =~ "D6" ]]; then
+		elif [[ ${sample} =~ "LCL6" ]]; then
 		    /opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL6.high.confidence.calls.vcf ${filtered_vcf} -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 			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 > ${sample}.reformed.vcf.gz
 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.reformed.vcf.gz
-	    elif [[ ${sample} =~ "F7" ]]; then
+	    elif [[ ${sample} =~ "LCL7" ]]; then
 	        /opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL7.high.confidence.calls.vcf ${filtered_vcf} -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 			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 > ${sample}.reformed.vcf.gz
 			/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${sample}.reformed.vcf.gz
-		elif [[ ${sample} =~ "M8" ]]; then
+		elif [[ ${sample} =~ "LCL8" ]]; then
 			/opt/hap.py/bin/hap.py /cromwell_root/tmp/reference_datasets_v202103/LCL8.high.confidence.calls.vcf ${filtered_vcf} -f /cromwell_root/tmp/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed --threads $nt -o ${sample} -r ${ref_dir}/${fasta}
 			cat ${filtered_vcf} | grep '##' > header
 			cat ${filtered_vcf} | grep -v '#' > body

tasks/rename_vcf.wdl

@@ -1,4 +1,4 @@
-task rename_fastq {
+task rename_vcf {
 
 	File vcf_D5
 	File vcf_D6

workflow.wdl

@@ -23,7 +23,7 @@ import "./tasks/merge_family.wdl" as merge_family
 import "./tasks/filter_vcf.wdl" as filter_vcf
 
 
-workflow {{ project_name }} {
+workflow project_name {
 
 	File? fastq_1_D5
 	File? fastq_1_D6