Test

defaults

@@ -15,6 +15,7 @@
     "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
     "database": "oss://pgx-reference-data/annovar_hg38/",
     "regions": "oss://pgx-reference-data/bed/cbcga/S07604514_Covered.bed",
+    "interval_padding": "10",
     "tnseq_pon": "",
     "tnscope_pon": "",
     "cosmic_vcf": "CosmicCodingMuts.hg38.v91.vcf",

inputs

@@ -21,6 +21,7 @@
   "{{ project_name }}.maftools_docker": "{{ maftools_docker }}",
   "{{ project_name }}.database": "{{ database }}",
   "{{ project_name }}.regions": "{{ regions }}",
+  "{{ project_name }}.interval_padding": "{{ interval_padding }}",
   "{{ project_name }}.tnseq_pon": "{{ tnseq_pon }}",
   "{{ project_name }}.tnscope_pon": "{{ tnscope_pon }}",
   "{{ project_name }}.cosmic_vcf": "{{ cosmic_vcf }}",

tasks/TNseq.wdl

@@ -22,9 +22,7 @@ task TNseq {
   String docker
   String cluster_config  
   String disk_size
-
   
-
   command <<<
     set -o pipefail
     set -e