test regions

inputs

@@ -4,13 +4,14 @@
   "{{ project_name }}.dbsnp": "dbsnp_146.hg38.vcf",
   "{{ project_name }}.recaled_bam": "{{ recaled_bam }}",
   "{{ project_name }}.SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
-  "{{ project_name }}.dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
   "{{ project_name }}.db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
   "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2020.10.07",
   "{{ project_name }}.dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
   "{{ project_name }}.sample": "{{ sample_id }}",
   "{{ project_name }}.disk_size": "500", 
-  "{{ project_name }}.recaled_bam_index": "{{ recaled_bam_index }}"
+  "{{ project_name }}.recaled_bam_index": "{{ recaled_bam_index }}",
+  "{{ project_name }}.regions": "oss://pgx-reference-data/bed/cbcga/S07604514_Covered.bed",
+  "{{ project_name }}.interval_padding": "0"
 }
 

tasks/Haplotyper.wdl

@@ -14,6 +14,9 @@ task Haplotyper {
 	String disk_size
 
 	File? regions
+	Int? interval_padding
+
+	String INTERVAL = if ${regions} then "--interval ${regions} --interval_padding ${interval_padding}" else ""
 
 command <<<
 		set -o pipefail
@@ -21,7 +24,7 @@ command <<<
 		export SENTIEON_LICENSE=192.168.0.55:8990
 		nt=$(nproc)	
 		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt \
-		-i ${recaled_bam} --interval ${regions} \
+		-i ${recaled_bam} ${INTERVAL} \
 		--algo Haplotyper -d ${dbsnp_dir}/${dbsnp} ${sample}_hc.vcf
 	>>>
 	

workflow.wdl

@@ -20,6 +20,7 @@ workflow {{ project_name }} {
 	String cluster_config
 
 	File? regions
+	Int? interval_padding
 
 	call Haplotyper.Haplotyper as Haplotyper {
 		input:
@@ -27,6 +28,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		ref_dir=ref_dir,
 		regions=regions,
+		interval_padding=interval_padding,
 		recaled_bam=recaled_bam,
 		recaled_bam_index=recaled_bam_index,
 		dbsnp=dbsnp,