bed

inputs

@@ -7,7 +7,7 @@
   "{{ project_name }}.LCL5": "{{ LCL5 }}",
   "{{ project_name }}.project": "{{ project }}",
   "{{ project_name }}.SMALLcluster_config": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",
-  "{{ project_name }}.bed": "oss://pgx-result/renluyao/manuscript_v3.0/reference_datasets_v202105/benchmark_regions.filtered.bed",
+  "{{ project_name }}.bed": "oss://pgx-result/renluyao/manuscript_v3.0/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed",
   "{{ project_name }}.BIGcluster_config": "OnDemand bcs.ps.g.2xlarge img-ubuntu-vpc",
   "{{ project_name }}.LCL6": "{{ LCL6 }}",
   "{{ project_name }}.sdf": "oss://pgx-reference-data/GRCh38.d1.vd1/GRCh38.d1.vd1.sdf/",

tasks/benchmark.wdl

@@ -4,8 +4,7 @@ task benchmark {
 	File contig
 	File sdf
 	File ref_dir
-	String fasta
-	String project
+	File fasta
 	String sample = basename(vcf,".vcf.gz")
 	String docker
 	String cluster_config

workflow.wdl

@@ -38,7 +38,6 @@ workflow {{ project_name }} {
 		contig=contig,
 		ref_dir=ref_dir,
 		fasta=fasta,
-		project=project,
 		docker=BENCHMARKdocker,
 		cluster_config=BIGcluster_config,
 		disk_size=disk_size,
@@ -52,7 +51,6 @@ workflow {{ project_name }} {
 		contig=contig,
 		ref_dir=ref_dir,
 		fasta=fasta,
-		project=project,
 		docker=BENCHMARKdocker,
 		cluster_config=BIGcluster_config,
 		disk_size=disk_size,
@@ -66,7 +64,6 @@ workflow {{ project_name }} {
 		contig=contig,
 		ref_dir=ref_dir,
 		fasta=fasta,
-		project=project,
 		docker=BENCHMARKdocker,
 		cluster_config=BIGcluster_config,
 		disk_size=disk_size,
@@ -80,7 +77,6 @@ workflow {{ project_name }} {
 		contig=contig,
 		ref_dir=ref_dir,
 		fasta=fasta,
-		project=project,
 		docker=BENCHMARKdocker,
 		cluster_config=BIGcluster_config,
 		disk_size=disk_size,