Update readme to match the additional of further taxonomic ranks to the bracken outputs

Author: mmac0026

docs/NextFlow/metagenomics.md

@@ -223,9 +223,13 @@ The main outputs of interest for downstream processing are your Bracken-correcte
 
 | Output | Description |
 | --- | --- |
-| `filtered_combined_bracken_report.tsv` | The Bracken-corrected clean counts table matrix |
+| `filtered_combined_bracken_report.tsv` | The Bracken-corrected clean counts table matrix including genus, family, order, class and phylum columns derived from the Kraken2/Bracken taxonomy database |
 | `decontam/` | A folder containing all of your trimmed, decontaminated `.fastq.gz` files – these can be used for other pipelines such as HUMAnN3 functional profiling. |
 
+!!! info "Additional taxonomy"
+
+    The filtering step requires access to the Kraken2/Bracken taxonomy files (`taxonomy/nodes.dmp` and `taxonomy/names.dmp`) to determine these higher-level ranks.
+
 **Folder structure**
 
 There are also a collection of quality control outputs and database files (if you didn't provide them to the pipeline) available in this directory too. If the pipeline generated the databases for you, it is recommended that you move these somewhere else so you can use them in future to save yourself some time. Below is an example of the output structure after running the pipeline.