Rename Taxonomic database section in schema to Taxnomic assignment, and move dada_min_boot there

Author: zmudge3

docs/usage.md

@@ -250,7 +250,7 @@ Special features of taxonomic classification tools:
 - QIIME2's reference taxonomy databases will have regions matching the amplicon extracted with primer sequences.
 - DADA2, Kraken2, and QIIME2 have specific parameters to accept custom databases (but theoretically possible with all classifiers)
 
-Parameter guidance is given in [nf-core/ampliseq website parameter documentation](https://nf-co.re/ampliseq/parameters/#taxonomic-database). Citations are listed in [`CITATIONS.md`](CITATIONS.md).
+Parameter guidance is given in [nf-core/ampliseq website parameter documentation](https://nf-co.re/ampliseq/parameters/#taxonomic-assignment). Citations are listed in [`CITATIONS.md`](CITATIONS.md).
 
 ### Multiple region analysis with Sidle
 

nextflow.config

@@ -119,10 +119,8 @@ params {
     skip_multiqc           = false
     skip_report            = false
 
-    // DADA2 assignTaxonomy options
+    // Taxonomic assignment options
     dada_min_boot = 50
-
-    // Database options
     dada_ref_taxonomy        = "silva=138.2"
     dada_assign_taxlevels    = null
     dada_ref_tax_custom      = null

nextflow_schema.json

@@ -405,29 +405,20 @@
             },
             "fa_icon": "fas fa-filter"
         },
-        "dada2_assigntaxonomy": {
-            "title": "DADA2 assignTaxonomy",
+        "taxonomic_assignment": {
+            "title": "Taxonomic assignment",
             "type": "object",
-            "description": "Options for the DADA2 assignTaxonomy method used to classify ASVs against a database",
-            "default": "",
-            "fa_icon": "fas fa-sitemap",
+            "fa_icon": "fas fa-database",
+            "description": "Choose a method and database for taxonomic assignments to single-region amplicons",
             "properties": {
                 "dada_min_boot": {
                     "type": "integer",
                     "default": 50,
                     "fa_icon": "fas fa-greater-than-equal",
-                    "description": "The minimum bootstrap confidence (out of 100 trials) for assigning a taxonomic level. Matches `minBoot` in DADA2's assignTaxonomy method.",
+                    "description": "The minimum bootstrap confidence (out of 100 trials) for assigning a taxonomic level with DADA2. Matches `minBoot` in DADA2's assignTaxonomy method.",
                     "minimum": 0,
                     "maximum": 100
-                }
-            }
-        },
-        "taxonomic_database": {
-            "title": "Taxonomic database",
-            "type": "object",
-            "fa_icon": "fas fa-database",
-            "description": "Choose a method and database for taxonomic assignments to single-region amplicons",
-            "properties": {
+                },
                 "dada_ref_taxonomy": {
                     "type": "string",
                     "help_text": "Choose any of the supported databases, and optionally also specify the version. Database and version are separated by an equal sign (`=`, e.g. `silva=138`) . This will download the desired database, format it to produce a file that is compatible with DADA2's assignTaxonomy and another file that is compatible with DADA2's addSpecies.\n\nThe following databases are supported:\n- GTDB - Genome Taxonomy Database - 16S rRNA\n- SBDI-GTDB, a Sativa-vetted version of the GTDB 16S rRNA\n- PR2 - Protist Reference Ribosomal Database - 18S rRNA\n- RDP - Ribosomal Database Project - 16S rRNA\n- SILVA ribosomal RNA gene database project - 16S rRNA\n- UNITE - eukaryotic nuclear ribosomal ITS region - ITS\n- COIDB - eukaryotic Cytochrome Oxidase I (COI) from The Barcode of Life Data System (BOLD) - COI\n\nGenerally, using `gtdb`, `pr2`, `rdp`, `sbdi-gtdb`, `silva`, `coidb`, `unite-fungi`, or `unite-alleuk` will select the most recent supported version.\n\nPlease note that commercial/non-academic entities [require licensing](https://www.arb-silva.de/silva-license-information) for SILVA v132 database (non-default) but not from v138 on (default).",
@@ -1109,10 +1100,7 @@
             "$ref": "#/$defs/asv_post_processing"
         },
         {
-            "$ref": "#/$defs/dada2_assigntaxonomy"
-        },
-        {
-            "$ref": "#/$defs/taxonomic_database"
+            "$ref": "#/$defs/taxonomic_assignment"
         },
         {
             "$ref": "#/$defs/multiregion_taxonomic_database"