added 2 new resfinder string outputs to TheiaProk workflows (FASTA, S…

…E, ONT). also added to export_taxon_tables inputs. renamed call block alias for resfinder in theiaprok_ONT to match other workflows
theiagen · Sep 20, 2023 · a2c727c · a2c727c
1 parent 32859d4
commit a2c727c
Show file tree

Hide file tree

Showing 3 changed files with 29 additions and 17 deletions.
diff --git a/workflows/theiaprok/wf_theiaprok_fasta.wdl b/workflows/theiaprok/wf_theiaprok_fasta.wdl
@@ -184,6 +184,8 @@ workflow theiaprok_fasta {
         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,
@@ -431,6 +433,8 @@ workflow theiaprok_fasta {
     File? resfinder_results = resfinder_task.resfinder_results_tab
     File? resfinder_pointfinder_pheno_table = resfinder_task.pointfinder_pheno_table
     File? resfinder_pointfinder_results = resfinder_task.pointfinder_results
+    String? resfinder_predicted_pheno_resistance = resfinder_task.resfinder_predicted_pheno_resistance
+    String? resfinder_predicted_xdr_shigella = resfinder_task.resfinder_predicted_xdr_shigella
     String? resfinder_db_version = resfinder_task.resfinder_db_version
     String? resfinder_docker = resfinder_task.resfinder_docker
     # MLST Typing

diff --git a/workflows/theiaprok/wf_theiaprok_illumina_se.wdl b/workflows/theiaprok/wf_theiaprok_illumina_se.wdl
@@ -282,6 +282,8 @@ workflow theiaprok_illumina_se {
             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,
@@ -577,6 +579,8 @@ workflow theiaprok_illumina_se {
     File? resfinder_results = resfinder_task.resfinder_results_tab
     File? resfinder_pointfinder_pheno_table = resfinder_task.pointfinder_pheno_table
     File? resfinder_pointfinder_results = resfinder_task.pointfinder_results
+    String? resfinder_predicted_pheno_resistance = resfinder_task.resfinder_predicted_pheno_resistance
+    String? resfinder_predicted_xdr_shigella = resfinder_task.resfinder_predicted_xdr_shigella
     String? resfinder_db_version = resfinder_task.resfinder_db_version
     String? resfinder_docker = resfinder_task.resfinder_docker
     # MLST Typing

diff --git a/workflows/theiaprok/wf_theiaprok_ont.wdl b/workflows/theiaprok/wf_theiaprok_ont.wdl
@@ -138,7 +138,7 @@ workflow theiaprok_ont {
           organism = select_first([expected_taxon, gambit.gambit_predicted_taxon])
       }
       if (call_resfinder) {
-        call resfinder_task.resfinder {
+        call resfinder_task.resfinder as resfinder_task {
           input:
             assembly = dragonflye.assembly_fasta,
             samplename = samplename,
@@ -274,14 +274,16 @@ workflow theiaprok_ont {
             amrfinderplus_amr_subclasses = amrfinderplus.amrfinderplus_amr_subclasses,
             amrfinderplus_version = amrfinderplus.amrfinderplus_version,
             amrfinderplus_db_version = amrfinderplus.amrfinderplus_db_version,
-            resfinder_pheno_table = resfinder.resfinder_pheno_table,
-            resfinder_pheno_table_species = resfinder.resfinder_pheno_table_species,
-            resfinder_seqs = resfinder.resfinder_hit_in_genome_seq,
-            resfinder_results = resfinder.resfinder_results_tab,
-            resfinder_pointfinder_pheno_table = resfinder.pointfinder_pheno_table,
-            resfinder_pointfinder_results = resfinder.pointfinder_results,
-            resfinder_db_version = resfinder.resfinder_db_version,
-            resfinder_docker = resfinder.resfinder_docker,
+            resfinder_pheno_table = resfinder_task.resfinder_pheno_table,
+            resfinder_pheno_table_species = resfinder_task.resfinder_pheno_table_species,
+            resfinder_seqs = resfinder_task.resfinder_hit_in_genome_seq,
+            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,
             ts_mlst_predicted_st = ts_mlst.ts_mlst_predicted_st,
             ts_mlst_pubmlst_scheme = ts_mlst.ts_mlst_pubmlst_scheme,
@@ -545,14 +547,16 @@ workflow theiaprok_ont {
     String? amrfinderplus_version = amrfinderplus.amrfinderplus_version
     String? amrfinderplus_db_version = amrfinderplus.amrfinderplus_db_version
     # Resfinder Outputs
-    File? resfinder_pheno_table = resfinder.resfinder_pheno_table
-    File? resfinder_pheno_table_species = resfinder.resfinder_pheno_table_species
-    File? resfinder_seqs = resfinder.resfinder_hit_in_genome_seq
-    File? resfinder_results = resfinder.resfinder_results_tab
-    File? resfinder_pointfinder_pheno_table = resfinder.pointfinder_pheno_table
-    File? resfinder_pointfinder_results = resfinder.pointfinder_results
-    String? resfinder_db_version = resfinder.resfinder_db_version
-    String? resfinder_docker = resfinder.resfinder_docker
+    File? resfinder_pheno_table = resfinder_task.resfinder_pheno_table
+    File? resfinder_pheno_table_species = resfinder_task.resfinder_pheno_table_species
+    File? resfinder_seqs = resfinder_task.resfinder_hit_in_genome_seq
+    File? resfinder_results = resfinder_task.resfinder_results_tab
+    File? resfinder_pointfinder_pheno_table = resfinder_task.pointfinder_pheno_table
+    File? resfinder_pointfinder_results = resfinder_task.pointfinder_results
+    String? resfinder_predicted_pheno_resistance = resfinder_task.resfinder_predicted_pheno_resistance
+    String? resfinder_predicted_xdr_shigella = resfinder_task.resfinder_predicted_xdr_shigella
+    String? resfinder_db_version = resfinder_task.resfinder_db_version
+    String? resfinder_docker = resfinder_task.resfinder_docker
     # MLST Typing
     File? ts_mlst_results = ts_mlst.ts_mlst_results
     String? ts_mlst_predicted_st = ts_mlst.ts_mlst_predicted_st