input

tasks/benchmark.wdl

@@ -3,6 +3,8 @@ task benchmark {
 	File benchmarking_dir
 	File contig
 	File sdf
+	File ref_dir
+	String fasta
 	String project
 	String sample = basename(vcf,".vcf.gz")
 	String docker

workflow.wdl

@@ -36,6 +36,8 @@ workflow {{ project_name }} {
 		benchmarking_dir=benchmarking_dir,
 		sdf=sdf,
 		contig=contig,
+		ref_dir=ref_dir,
+		fasta=fasta,
 		project=project,
 		docker=BENCHMARKdocker,
 		cluster_config=BIGcluster_config,
@@ -48,6 +50,8 @@ workflow {{ project_name }} {
 		benchmarking_dir=benchmarking_dir,
 		sdf=sdf,
 		contig=contig,
+		ref_dir=ref_dir,
+		fasta=fasta,
 		project=project,
 		docker=BENCHMARKdocker,
 		cluster_config=BIGcluster_config,
@@ -60,6 +64,8 @@ workflow {{ project_name }} {
 		benchmarking_dir=benchmarking_dir,
 		sdf=sdf,
 		contig=contig,
+		ref_dir=ref_dir,
+		fasta=fasta,
 		project=project,
 		docker=BENCHMARKdocker,
 		cluster_config=BIGcluster_config,
@@ -72,6 +78,8 @@ workflow {{ project_name }} {
 		benchmarking_dir=benchmarking_dir,
 		sdf=sdf,
 		contig=contig,
+		ref_dir=ref_dir,
+		fasta=fasta,
 		project=project,
 		docker=BENCHMARKdocker,
 		cluster_config=BIGcluster_config,