added 2 new resfinder string outputs to theiaprok_illumina_pe workflo…

…w as well as export_taxon_tables task
theiagen · Sep 20, 2023 · 32859d4 · 32859d4
1 parent d17db06
commit 32859d4
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diff --git 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
@@ -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,