Update user guide

docs/user_guide/templates.md

@@ -1,3 +1,64 @@
 # Project and stage templates
 
-TODO
+DSO provides a templating engine that allows to quickly bootrstap a project (`dso init`), folder, or stages (`dso create`).
+Templates are based on [jinja2](https://jinja.palletsprojects.com/en/stable/templates/).
+
+## Available templates
+
+DSO currently comes with the following templates:
+
+Project templates:
+
+-   [default](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates/init/default) - Default template, with
+    integration of `git`, `dvc`, `uv`, `pre-commit`, and `editorconfig`.
+
+Folder templates:
+
+-   [default](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates/folder/default) - This one is very minimal, just a folder with `dvc.yaml` and `params.in.yaml` files.
+
+Stage templates:
+
+-   [quarto](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates/stage/quarto) - Template for quarto notebook in R
+-   [bash](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates/stage/bash) - Template for executing a bash snippet
+
+The source code of the templates can be [inspected on GitHub](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates).
+Templates shipped with DSO are [licensed](https://github.com/Boehringer-Ingelheim/dso/blob/main/src/dso/templates/LICENSE) under the Creative Commons Zero v1.0
+Universal license.
+
+## Using custom template libraries
+
+Currently, dso only supports the internal templates mentioned above. However, we plan to add support to custom
+stage templates soon. This enables some interesting use-cases:
+
+-   Organization-specific templates: Use templates that make it easier to comply with internal processes or apply
+    corporate design.
+-   Best-practice codebases: Start off common analysis types off a predefined template. We believe that some analyses
+    require more flexibility than predefined worflows such as nf-core, but can still benefit from a structured
+    "base" document to get started with.
+
+## Writing templates
+
+Template directories are recursively copied to their destination and files are rendered with [jinja2](https://jinja.palletsprojects.com/en/stable/templates/).
+You can use all features of jinja2 such as `if/else` blocks or loops. Additionally, you have access to the
+following variables:
+
+Available variables for **project** templates:
+
+| variable            | content                                               |
+| ------------------- | ----------------------------------------------------- |
+| project_name        | project/folder name as provided to the `dso init` CLI |
+| project_description | description as provided to the `dso init` CLI         |
+
+Available variables for **folder** templates:
+
+| variable    | content                                                |
+| ----------- | ------------------------------------------------------ |
+| folder_name | folder name as provided to the `dso create folder` CLI |
+
+Available variables for **stage** templates:
+
+| variable          | content                                               |
+| ----------------- | ----------------------------------------------------- |
+| stage_name        | folder name as provided to the `dso create stage` CLI |
+| stage_description | description as provided to the `dso create stage` CLI |
+| stage_path        | Path to the stage relative to the project root        |

src/dso/cli/_create.py

@@ -96,7 +96,7 @@ def dso_create_folder(name: str | None = None):
 
     target_dir.mkdir(exist_ok=True)
 
-    instantiate_template(get_template_path("folder", template), target_dir, stage_name=name)
+    instantiate_template(get_template_path("folder", template), target_dir, folder_name=name)
     log.info("[green]Folder created successfully.")
     compile_all_configs([target_dir])