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https://github.com/carpentries-incubator/snakemake-novice-bioinformatics

Introduction to Snakemake for Bioinformatics
https://github.com/carpentries-incubator/snakemake-novice-bioinformatics

bioinformatics carpentries-incubator english lesson pre-alpha snakemake workflows

Last synced: 5 days ago
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Introduction to Snakemake for Bioinformatics

Host: GitHub
URL: https://github.com/carpentries-incubator/snakemake-novice-bioinformatics
Owner: carpentries-incubator
License: other
Created: 2021-03-25T12:29:17.000Z (almost 4 years ago)
Default Branch: main
Last Pushed: 2024-12-17T01:07:07.000Z (17 days ago)
Last Synced: 2024-12-17T02:23:00.469Z (17 days ago)
Topics: bioinformatics, carpentries-incubator, english, lesson, pre-alpha, snakemake, workflows
Language: Python
Homepage: https://carpentries-incubator.github.io/snakemake-novice-bioinformatics
Size: 9.71 MB
Stars: 19
Watchers: 6
Forks: 9
Open Issues: 24
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION
- Authors: AUTHORS

Awesome Lists containing this project

README

# Snakemake for Bioinformatics

[![The Carpentries Lab Review Status](https://badges.carpentries-lab.org/17_status.svg)](https://github.com/carpentries-lab/reviews/issues/17)

## 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](https://snakemake.readthedocs.io/):

> 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.

## 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](CONTRIBUTING.md) and have a look at
the [more detailed guidelines][lesson-example] on proper formatting, ways to render the lesson locally, and even
how to write new episodes.

Please see the current list of [issues](https://github.com/carpentries-incubator/snakemake-novice-bioinformatics/issues)
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](https://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project) in Pro Git
by Scott Chacon.
Look for the tag ![good\_first\_issue](https://img.shields.io/badge/-good%20first%20issue-gold.svg). This indicates that the maintainers
will welcome a pull request fixing this issue.

## Maintainer(s)

Current maintainers of this lesson are

- [Tim Booth](https://github.com/tbooth)
- [Graeme Grimes](https://github.com/ggrimes)