Using frogs databases

tools/dada2_assign_taxonomy/dada2_assign_taxonomy.rule.snakefile

@@ -7,12 +7,12 @@ rule <step_name>__dada2_assign_taxonomy:
     params:
         output_dir = config["results_dir"] + "/" + config["<step_name>__dada2_assign_taxonomy_output_dir"],
         step_dir = config["<step_name>__dada2_assign_taxonomy_output_dir"],
-        script = config["<step_name>__dada2_assign_taxonomy_script"]
+        script = config["<step_name>__dada2_assign_taxonomy_script"],
         #taxonomypath = config["<step_name>__dada2_assign_taxonomy_taxonomypath"],
         
         taxonomypath = config["<step_name>__dada2_assign_taxonomy_reference_fasta"],
         taxfile = config["<step_name>__dada2_assign_taxonomy_reference_fasta"]+"/train_set.fasta",
-        yamlfile = config["<step_name>__FROGS_assign_taxonomy_reference_fasta"]+"/info.yaml",
+        yamlfile = config["<step_name>__dada2_assign_taxonomy_reference_fasta"]+"/info.yaml",
 
         #OTUabundance = config["<step_name>__dada2_assign_taxonomy_abundance"],
         richness = config["results_dir"] + "/" + config["<step_name>__dada2_assign_taxonomy_output_dir"] + "/richness_mqc.png",
@@ -25,5 +25,5 @@ rule <step_name>__dada2_assign_taxonomy:
         config["results_dir"]+'/logs/' + config["<step_name>__dada2_assign_taxonomy_output_dir"] + '/dada2_assign_taxonomy_log.txt'
     script:
         config["<step_name>__dada2_assign_taxonomy_script"]
-        
+
     
\ No newline at end of file

tools/dada2_assign_taxonomy/dada2_assign_taxonomy.yaml

@@ -66,24 +66,6 @@
               value: "/FROGS_taxonomy/SILVA/16S",
               label: "Taxonomy source"
             },
-            {
-              name: dada2_assign_taxonomy_taxonomypath,
-              type: select,
-              choices: [
-                silva138 (16S): "/taxonomy/silva138",
-                silva132 (16S): "/taxonomy/silva132",
-                silva128 (16S): "/taxonomy/silva128",
-                rdp16 (16S): "/taxonomy/rdp16",
-                greengenes13.8 (16S): "/taxonomy/gg13_8",
-                unite_8.2 (ITS):  "/taxonomy/unite_8.2",
-                unite_2_2_2019 (ITS):  "/taxonomy/unite_2_2_2019",
-                midori_COI (COI): "/taxonomy/midori_coi",
-                midori_COI_Without_Terrestrial (COI): "/taxonomy/midori_coi_wo_terrestrial",
-                refseq-rdp16s (16S): "/taxonomy/refseq-rdp16s"
-              ],
-              value: "silva138 (16S)",
-              label: "Taxonomy source"
-            },
             {
               name: dada2_assign_taxonomy_tryRC,
               prefix: ,
@@ -154,6 +136,9 @@
     krona: [
       "Ondov BD, Bergman NH, and Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30; 12(1):385"
     ],
+    frogs: [
+      "Maria Bernard, Olivier Rué, Mahendra Mariadassou and Géraldine Pascal; FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers, Briefings in Bioinformatics 2021, 10.1093/bib/bbab318 "
+    ]
 
   }
 }