fix docs

README.md

@@ -34,7 +34,7 @@ The pipeline performs the following steps:
 2. **Guide Tree**: (Optional) Renders a guide tree with a chosen tool (list available in [usage](docs/usage.md#2-guide-trees)). Some aligners use guide trees to define the order in which the sequences are aligned.
 3. **Align**: (Required) Aligns the sequences with a chosen tool (list available in [usage](docs/usage.md#3-align)).
 4. **Evaluate**: (Optional) Evaluates the generated alignments with different metrics: Sum Of Pairs (SoP), Total Column score (TC), iRMSD, Total Consistency Score (TCS), etc.
-5. **Report**: Reports the collected information of the runs in a Shiny app and a summary table in MultiQC.
+5. **Report**: Reports the collected information of the runs in a Shiny app and a summary table in MultiQC. Optionally, it can also render the [Foldmason](https://github.com/steineggerlab/foldmason) MSA visualization in html format.
 
 ## Usage
 

docs/usage.md

@@ -91,6 +91,8 @@ The provided structures (see samplesheet) are used to evaluate the quality of th
 Finally, a summary table with all the computed statistics and evaluations is reported in MultiQC (skip by using `--skip_multiqc`).
 Moreover, a Shiny app is generated with interactive summary plots (skip with `--skip_shiny`).
 
+If structures are provided, the [Foldmason](https://github.com/steineggerlab/foldmason) visualizatin will be rendered (skip with `--skip_visualisation`).
+
 :::warning
 You will need to have [Shiny](https://shiny.posit.co/py/) installed to run it! See [output documentation](https://nf-co.re/multiplesequencealign/output) for more info.
 :::