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Snakemake for Bioinformatics

TODO - get this listed on the Community Developed Lessons page once ready.

Snakemake for Bioinformatics

This lesson introduces the Snakemake workflow system in the context of a bioinformatics data analysis task.

To quote from the official Snakemake documentation:

The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.

Snakemake originated as, and remains most popular as, a tool for bioinformatics. This is how we present it here. However, Snakemake is a general-purpose system and may be used for all manner of data processing tasks.

Snakemake is a superset of the Python language and as such can draw on the full power of Python, but you do not need to be a Python programmer to use it. This lesson assumes no prior knowledge of Python and intruduces just a few concepts as needed to construct useful workflows.

Lesson development checklist

Before you begin developing your new lesson, here are a few things we recommend you do:

* To set the URL on GitHub, click the gear wheel button next to About on the right of the repository landing page. The lesson URL structure is https://carpentries-incubator.github.io/<repository-slug>: a repository at https://github.com/carpentries-incubator/new-lesson/ will have pages at the lesson URL https://carpentries-incubator.github.io/new-lesson/.

Contributing

We welcome all contributions to improve the lesson! Maintainers will do their best to help you if you have any questions, concerns, or experience any difficulties along the way.

We'd like to ask you to familiarize yourself with our Contribution Guide and have a look at the more detailed guidelines on proper formatting, ways to render the lesson locally, and even how to write new episodes.

Please see the current list of [issues][FIXME] for ideas for contributing to this repository. For making your contribution, we use the GitHub flow, which is nicely explained in the chapter Contributing to a Project in Pro Git by Scott Chacon. Look for the tag good_first_issue. This indicates that the maintainers will welcome a pull request fixing this issue.

Maintainer(s)

Current maintainers of this lesson are

Authors

A list of contributors to the lesson can be found in AUTHORS

Citation

To cite this lesson, please consult with CITATION

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