debug

tasks/benchmark.wdl

@@ -1,9 +1,9 @@
 task benchmark {
-	File vcf
+	File filtered_vcf
 	File benchmarking_dir
 	File ref_dir
 	File? qc_bed
-	String sample = basename(vcf,".hc.vcf")
+	String sample = basename(filtered_vcf,".filtered.vcf")
 	String fasta
 	String docker
 	String cluster_config
@@ -20,7 +20,7 @@ task benchmark {
 
 		export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa
 
-		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip ${vcf} -c > ${sample}.rtg.vcf.gz
+		/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
 
 		if [ ${qc_bed} ];then

tasks/filter_vcf_bed.wdl

@@ -32,6 +32,6 @@
 	}
 	output {
 		File filtered_vcf = "${project}.filtered.vcf"
-		File? filtered_bed = "benchmark_region_query_bed.bed"
+		Array[File] filtered_bed = glob("benchmark_region_query_bed.bed")
 	}
 }

workflow.wdl

@@ -764,7 +764,7 @@ workflow {{ project_name }} {
 
 		call benchmark.benchmark as benchmark_D5_vcf {
 			input:
-			vcf=filter_vcf_bed_D5_vcf.filtered_vcf,
+			filtered_vcf=filter_vcf_bed_D5_vcf.filtered_vcf,
 			benchmarking_dir=benchmarking_dir,
 			ref_dir=ref_dir,
 			qc_bed=filter_vcf_bed_D5.filtered_bed,
@@ -787,7 +787,7 @@ workflow {{ project_name }} {
 
 		call benchmark.benchmark as benchmark_D6_vcf {
 			input:
-			vcf=filter_vcf_bed_D6.filtered_vcf,
+			filtered_vcf=filter_vcf_bed_D6.filtered_vcf,
 			benchmarking_dir=benchmarking_dir,
 			ref_dir=ref_dir,
 			qc_bed=filter_vcf_bed_D6.filtered_bed,
@@ -810,7 +810,7 @@ workflow {{ project_name }} {
 
 		call benchmark.benchmark as benchmark_F7_vcf {
 			input:
-			vcf=filter_vcf_bed_F7_vcf.filtered_vcf,
+			filtered_vcf=filter_vcf_bed_F7_vcf.filtered_vcf,
 			benchmarking_dir=benchmarking_dir,
 			ref_dir=ref_dir,
 			qc_bed=filter_vcf_bed_F7.filtered_bed,
@@ -833,7 +833,7 @@ workflow {{ project_name }} {
 
 		call benchmark.benchmark as benchmark_M8_vcf {
 			input:
-			vcf=filter_vcf_bed_M8_vcf.filtered_vcf,
+			filtered_vcf=filter_vcf_bed_M8_vcf.filtered_vcf,
 			benchmarking_dir=benchmarking_dir,
 			ref_dir=ref_dir,
 			qc_bed=filter_vcf_bed_M8.filtered_bed,