diff --git a/tasks/utilities/task_broad_terra_tools.wdl b/tasks/utilities/task_broad_terra_tools.wdl index b585d73f2..bd2030088 100644 --- a/tasks/utilities/task_broad_terra_tools.wdl +++ b/tasks/utilities/task_broad_terra_tools.wdl @@ -110,6 +110,8 @@ task export_taxon_tables { File? resfinder_results File? resfinder_pointfinder_pheno_table File? resfinder_pointfinder_results + String? resfinder_predicted_pheno_resistance + String? resfinder_predicted_xdr_shigella String? resfinder_db_version String? resfinder_docker File? ts_mlst_results @@ -593,6 +595,8 @@ task export_taxon_tables { "resfinder_results": "~{resfinder_results}", "resfinder_pointfinder_pheno_table": "~{resfinder_pointfinder_pheno_table}", "resfinder_pointfinder_results": "~{resfinder_pointfinder_results}", + "resfinder_predicted_pheno_resistance": "~{resfinder_predicted_pheno_resistance}", + "resfinder_predicted_xdr_shigella": "~{resfinder_predicted_xdr_shigella}", "resfinder_db_version": "~{resfinder_db_version}", "resfinder_docker": "~{resfinder_docker}", "prokka_gff": "~{prokka_gff}", diff --git a/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl index 2fa51347a..8eb202b43 100644 --- a/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl +++ b/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl @@ -309,6 +309,8 @@ workflow theiaprok_illumina_pe { resfinder_results = resfinder_task.resfinder_results_tab, resfinder_pointfinder_pheno_table = resfinder_task.pointfinder_pheno_table, resfinder_pointfinder_results = resfinder_task.pointfinder_results, + resfinder_predicted_pheno_resistance = resfinder_task.resfinder_predicted_pheno_resistance, + resfinder_predicted_xdr_shigella = resfinder_task.resfinder_predicted_xdr_shigella, resfinder_db_version = resfinder_task.resfinder_db_version, resfinder_docker = resfinder_task.resfinder_docker, ts_mlst_results = ts_mlst.ts_mlst_results,