Updated docs

docs/index.md

@@ -3,6 +3,7 @@
 [![](https://img.shields.io/static/v1?label=CLI&message=Snaketool&color=blueviolet)](https://github.com/beardymcjohnface/Snaketool)
 [![license](https://img.shields.io/github/license/metagenlab/assembly_finder.svg)](https://github.com/metagenlab/assembly_finder/blob/main/LICENSE)
 [![version](https://img.shields.io/conda/v/bioconda/assembly_finder?label=version)](http://bioconda.github.io/recipes/assembly_finder/README.html)
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/assembly_finder/README.html)
 [![downloads](https://img.shields.io/conda/dn/bioconda/assembly_finder)](https://anaconda.org/bioconda/assembly_finder)
 [![tests](https://github.com/metagenlab/assembly_finder/actions/workflows/unit-tests.yml/badge.svg)](https://github.com/metagenlab/assembly_finder/actions/workflows/unit-tests.yml)
 [![docs](https://github.com/metagenlab/assembly_finder/actions/workflows/build-docs.yml/badge.svg)](https://github.com/metagenlab/assembly_finder/actions/workflows/build-docs.yml)
@@ -11,17 +12,47 @@ Assembly finder is a Snakemake-powered cli to download genomes with [NCBI datase
 
 ## Installation
 
-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/assembly_finder/README.html)
+=== "mamba <small>(recommended)</small>" 
 
-```sh
-mamba create -n assembly_finder assembly_finder
-```
+    ```sh
+    mamba create -n assembly_finder assembly_finder
+    ```
+    !!! note
+        Requires a [mamba](https://github.com/conda-forge/miniforge) installation
+=== "docker" 
+
+    ```sh
+    docker pull ghcr.io/metagenlab/assembly_finder:latest
+    ```
+
+    !!! note
+        Add `--no-use-conda` when using the container
+
+=== "git" 
+
+    ```sh
+    git clone https://github.com/metagenlab/assembly_finder.git
+    pip install -e assembly_finder
+    ```
+    !!! note
+        Requires a [mamba](https://github.com/conda-forge/miniforge) installation
 
-## Example
+## Usage 
 ### Command
-```sh
-assembly_finder -i staphylococcus_aureus -nb 1 
-```
+
+=== "standard"
+
+    ```sh
+    assembly_finder -i staphylococcus_aureus -nb 1 
+    ```
+
+=== "container"
+
+    ```sh
+    docker run ghcr.io/metagenlab/assembly_finder:latest \
+    assembly_finder -i staphylococcus_aureus -nb 1 --no-use-conda
+    ```
+
 ### Output
 ```sh
 📂staphylococcus_aureus
@@ -44,6 +75,6 @@ assembly_finder -i staphylococcus_aureus -nb 1
  ┗ 📜taxonomy.tsv
 ```
 
-## Usage
+## Command-line options
 
 ![`assembly_finder -h`](images/af-help.svg)