Project and stage templates

Project and stage templates#

DSO provides a templating engine that allows to quickly boostrap a project (dso init), folder, or stages (dso create). Templates are based on jinja2.

Available templates#

DSO currently comes with the following templates:

Project templates:

  • default - Default template, with integration of git, dvc, uv, pre-commit, and editorconfig.

Folder templates:

  • default - This one is very minimal, just a folder with dvc.yaml and params.in.yaml files.

Stage templates:

  • quarto_r - Template for quarto notebook in R

  • quarto_py - Template for quarto notebook in Python (quarto markdown (.qmd) format)

  • quarto_r - Template for quarto notebook in Python (jupyter notebook (.ipynb) format)

  • bash - Template for executing a bash snippet

The source code of the templates can be inspected on GitHub. Templates shipped with DSO are licensed 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 (#9). 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. 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