update docs

Author: d4straub

CHANGELOG.md

@@ -19,6 +19,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Dependencies`
 
+- [#936](https://github.com/nf-core/ampliseq/pull/936) - Updated some software versions
+
+| software | previously | now    |
+| -------- | ---------- | ------ |
+| Cutadapt | 4.6        | 5.2    |
+| DADA2    | 1.30.0     | 1.34.0 |
+| Phyloseq | 1.46.0     | 1.50.0 |
+| MultiQC  | 1.29       | 1.33   |
+
 ### `Removed`
 
 ## nf-core/ampliseq version 2.15.0 - 2025-10-06

docs/output.md

@@ -194,6 +194,7 @@ Optionally, ASV sequences can be filtered for rRNA sequences identified by Barrn
 - `barrnap/`
   - `rrna.<kingdom>.gff`: GFF3 output for rRNA matches per kingdom, where kingdom is one of `bac,arc,mito,euk`.
   - `summary.tsv`: Summary of evalues for each ASV and kingdom
+  - `result.tsv`: Classification of ASVs into kindoms based on the lowest evalue, only if `--filter_ssu` is set.
   - `ASV_seqs.ssu.fasta`: Fasta file with filtered ASV sequences, only if `--filter_ssu` is set.
   - `ASV_table.ssu.tsv`: Counts for each filtered ASV sequence, only if `--filter_ssu` is set.
   - `stats.ssu.tsv`: Tracking read numbers through filtering, for each sample, only if `--filter_ssu` is set.