eclarke / sbx_template

Template for Sunbeam extensions.

Sunbeam extension template

This is a template to use to extend the Sunbeam pipeline. There are three major parts to a Sunbeam extension:

• requirements.txt specifies the extension's dependencies
• config.yml contains configuration options that can be specified by the user when running an extension
• sbx_template.rules contains the rules (logic/commands run) of the extension

Creating an extension

Any dependencies required for an extension should be listed in the requirements.txt file in the standard requirement format.

The config.yml contains parameters that the user might need to modify when running an extension. For example, if your downstream analysis is run differently depending on whether reads are paired- or single-end, it would probably be wise to include a paired_end parameter. Default values should be specified for each bottom-level key.

Finally, sbx_template.rules contains the actual logic for the extension, including required input and output files. A detailed discussion of Snakemake rule creation is beyond the scope of this tutorial, but definitely check out the Snakemake tutorial and any of the extensions by sunbeam-labs for inspiration.

Installing an extension

Installing an extension is as simple as cloning (or moving) your extension directory into the sunbeam/extensions/ folder, installing requirements through Conda, and adding the new options to your existing configuration file:

git clone https://github.com/louiejtaylor/sbx_template/ sunbeam/extensions/sbx_template
conda install --file sunbeam/extensions/sbx_template/requirements.txt
cat sunbeam/extensions/sbx_template/config.yml >> sunbeam_config.yml

Running an extension

To run an extension, simply run Sunbeam as usual with your extension's target rule specified:

sunbeam run --configfile=sunbeam_config.yml example_rule