Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <[email protected]>
nf-core · dialvarezs · Jun 2, 2025 · May 9, 2025 · May 12, 2025 · May 15, 2025
commit 21b3ed6436136821a5f8320a5f31ae32383e2832
@@ -142,7 +142,9 @@ This database can be downloaded from the [CAT developers' website](https://tbb.b
 > [!NOTE]
 > By default, the pipeline will use the `NCBI nr` database.
 
-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`.
+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`.
 
 ### GTDB
 

@@ -519,12 +519,12 @@
                 "cat_allow_unofficial_lineages": {
                     "type": "boolean",
                     "description": "Allow unofficial lineages in CAT classification.",
-                    "help_text": "By default, CAT uses only official lineages for classification. This option enables unofficial lineages, which is useful with custom databases.\n\nNote that it disables classification result summarization, as this is not supported."
+                    "help_text": "By default, CAT uses only official lineages for classification. This option enables unofficial lineages, which is useful with custom databases.\n\nNote that it disables classification result summarization, as this is not supported by CAT_pack summarise."
                 },
                 "cat_classify_unbinned": {
                     "type": "boolean",
                     "description": "Classify unbinned contigs with CAT (contig mode).",
-                    "help_text": "This will run CAT classification on all unbinned contigs, which can be useful to get an idea of the taxonomic composition of the unbinned contigs. In some cases this may extend run time of the pipeline."
+                    "help_text": "By default, nf-core/mag only runs CAT taxonomic classification on bins. Specifying this parameter will  additionally run CAT classification on all unbinned contigs, which can be useful to get an idea of the taxonomic composition of the unbinned contigs. In some cases this may significantly extend run time of the pipeline."
                 },
                 "skip_gtdbtk": {
                     "type": "boolean",