Linting fixes

Author: dialvarezs

.vscode/settings.json

@@ -1,24 +1,3 @@
 {
-    "markdown.styles": [
-        "public/vscode_markdown.css"
-    ],
-    "workbench.colorCustomizations": {
-        "activityBar.activeBackground": "#2f7b49",
-        "activityBar.background": "#2f7b49",
-        "activityBar.foreground": "#e7e7e7",
-        "activityBar.inactiveForeground": "#e7e7e799",
-        "activityBarBadge.background": "#442c73",
-        "activityBarBadge.foreground": "#e7e7e7",
-        "commandCenter.border": "#e7e7e799",
-        "sash.hoverBorder": "#2f7b49",
-        "statusBar.background": "#215633",
-        "statusBar.foreground": "#e7e7e7",
-        "statusBarItem.hoverBackground": "#2f7b49",
-        "statusBarItem.remoteBackground": "#215633",
-        "statusBarItem.remoteForeground": "#e7e7e7",
-        "titleBar.activeBackground": "#215633",
-        "titleBar.activeForeground": "#e7e7e7",
-        "titleBar.inactiveBackground": "#21563399",
-        "titleBar.inactiveForeground": "#e7e7e799"
-    }
+    "markdown.styles": ["public/vscode_markdown.css"]
 }

CHANGELOG.md

@@ -10,13 +10,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#799](https://github.com/nf-core/mag/pull/799) - Add `--cat_classify_unbinned`, to enable taxonomic classification of unbinned contigs using CAT (by @dialvarezs)
 
 ### `Changed`
+
 - [#799](https://github.comf/nf-core/mag/pull/799) - Migrate from local CAT modules to nf-core ones, updating version (by @dialvarezs)
 
 ### `Dependencies`
 
-| Tool    | Previous version | New version |
-| ------- | ---------------- | ----------- |
-| CAT     | 5.2.3            | 6.0.1       |
+| Tool | Previous version | New version |
+| ---- | ---------------- | ----------- |
+| CAT  | 5.2.3            | 6.0.1       |
 
 ## v4.0.0 - [2025-05-22]
 

docs/usage.md

@@ -140,7 +140,7 @@ You can also pass to `--busco_db` a URL pointing to a lineage tarball, or the ta
 This database can be downloaded from the [CAT developers' website](https://tbb.bio.uu.nl/tina/CAT_pack_prepare/), which is based in the Netherlands (and could be slow for other regions of the world).
 
 > [!NOTE]
-Only the `CAT_nr` database is supported by the pipeline.
+> Only the `CAT_nr` database is supported by the pipeline.
 
 Enabling the `--cat_db_generate` option will create a new database using the latest version of the NCBI nr database. This requires a large download (over 200 GB) and several hours of subsequent processing. If you enable the `--save_cat_db` option, the database will be saved in the `Taxonomy/CAT/db` directory and can be reused in future runs by specifying its path with `--cat_db`.