Add germline-resource.tbi

defaults

@@ -8,6 +8,7 @@
     "dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
     "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
     "germline_resource": "oss://pgx-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz",
+    "germline_resource_tbi": "oss://pgx-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz.tbi",
     "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2020.10.07",
     "varscan_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/varscan2:v2.4.3",
     "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2018.04",

inputs

@@ -15,6 +15,7 @@
   "{{ project_name }}.dbmills_dir": "{{ dbmills_dir }}",
   "{{ project_name }}.db_mills": "{{ db_mills }}",
   "{{ project_name }}.germline_resource": "{{ germline_resource }}",
+  "{{ project_name }}.germline_resource_tbi": "{{ germline_resource_tbi }}",
   "{{ project_name }}.sentieon_docker": "{{ sentieon_docker }}",
   "{{ project_name }}.varscan_docker": "{{ varscan_docker }}",
   "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",

tasks/TNseq.wdl

@@ -15,6 +15,7 @@ task TNseq {
   File ref_dir
   String fasta
   File germline_resource
+  File germline_resource_tbi
   File? regions
   Int? interval_padding
   File? pon_vcf
@@ -22,7 +23,7 @@ task TNseq {
   String docker
   String cluster_config  
   String disk_size
-  
+
   command <<<
     set -o pipefail
     set -e

workflow.wdl

@@ -25,6 +25,7 @@ workflow {{ project_name }} {
     File dbsnp_dir
     String dbsnp
     File germline_resource
+    File germline_resource_tbi
     
     File? regions
     Int? interval_padding
@@ -62,6 +63,7 @@ workflow {{ project_name }} {
             regions=regions,
             interval_padding=interval_padding,
             germline_resource=germline_resource,
+            germline_resource_tbi=germline_resource_tbi,
             pon_vcf=tnseq_pon,
             docker=sentieon_docker,
             cluster_config=cluster_config,