```{include} ../README.md
```

```{toctree}
:caption: Getting Started
:name: getting_started
:hidden:
:maxdepth: 2

getting_started/installation
getting_started/docker
getting_started/apptainer
getting_started/conda
```

```{toctree}
:caption: Usage Notes
:name: usage
:hidden:
:maxdepth: 2

usage/cli
usage/useful_options
```

```{toctree}
:caption: Workflow Details
:name: workflow_details
:hidden:
:maxdepth: 2

workflow/workflow
```

```{toctree}
:caption: Outputs of Autoafids
:name: outputs
:hidden:
:maxdepth: 2

outputs/output_files
```

```{toctree}
:caption: Contributing
:name: contributing
:hidden:
:maxdepth: 2

contributing/contributing
```