diff --git a/docs/snakefiles/deployment.rst b/docs/snakefiles/deployment.rst index e9c9060eb..bd06f846b 100644 --- a/docs/snakefiles/deployment.rst +++ b/docs/snakefiles/deployment.rst @@ -37,7 +37,7 @@ following structure: In other words, the workflow code goes into a subfolder ``workflow``, while the configuration is stored in a subfolder ``config``. Inside of the ``workflow`` subfolder, the central ``Snakefile`` marks the entrypoint of the workflow (it will be automatically discovered when running snakemake from the root of above structure. -This main structure and the recommendations below are implemented in `this Snakemake workflow template `_ that you can use to `create your own workflow repository with a single click on "Use this template" _. +This main structure and the recommendations below are implemented in `this Snakemake workflow template `_ that you can use to `create your own workflow repository with a single click on "Use this template" `_. In addition to the central ``Snakefile``, rules can be stored in a modular way, using the optional subfolder ``workflow/rules``. Such modules should end with ``.smk``, the recommended file extension of Snakemake. Further, :ref:`scripts ` should be stored in a subfolder ``workflow/scripts`` and notebooks in a subfolder ``workflow/notebooks``.