add docs

docs/output.md

@@ -163,6 +163,26 @@ The summary file lists all statistics of kraken2 and/or bbduk (and optionally bl
 
 Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
 
+### Downstream samplesheets
+
+The pipeline can also generate input files for the following downstream
+pipelines:
+
+- [nf-core/taxprofiler](https://nf-co.re/taxprofiler)
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `downstream_samplesheets/`
+  - `taxprofiler.csv`: Filled out nf-core/taxprofiler `--input` csv with paths to reads relative to the results directory
+
+</details>
+
+:::warning
+Any generated downstream samplesheet is provided as 'best effort' and are not guaranteed to work straight out of the box!
+They may not be complete (e.g. some columns may need to be manually filled in).
+:::
+
 ### Pipeline information
 
 <details markdown="1">