https://github.com/doi-usgs/snakemake-introduction
https://github.com/doi-usgs/snakemake-introduction
Last synced: about 1 month ago
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- Host: GitHub
- URL: https://github.com/doi-usgs/snakemake-introduction
- Owner: DOI-USGS
- License: other
- Created: 2022-06-22T16:48:42.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2024-04-02T21:12:15.000Z (about 1 year ago)
- Last Synced: 2025-03-29T09:12:36.284Z (about 2 months ago)
- Language: Python
- Size: 79.1 KB
- Stars: 8
- Watchers: 8
- Forks: 8
- Open Issues: 11
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Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: CODE_OF_CONDUCT.md
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README
# Introduction to Snakemake Tutorial
This tutorial introduces the use of Snakemake as a pipelining tool for Python code. It explains some general Snakemake concepts and gives an opportunity to implement them on a small water-related example problem.
The tutorial is organized as an ordered set of lessons, each of which introduces new Snakemake concepts. Each lesson is contained in a markdown file in the `issues` folder of this repository. The rest of the code contained in the repository is the codebase you will start from and modify as you go through each lesson.
In order to walk through this tutorial, fork this repository into your own GitHub account. Then, clone your fork onto your local computer to work on.
To begin the tutorial, open the markdown file [`issues/issue_0.md`](issues/issue_0.md) in GitHub. Issue 0 takes you through some basic setup and installation. You can then proceed through the following issues to continue through the tutorial.
For every issue (except issue 0), you will be making changes to the code in the repository. If you are working with an instructor for this tutorial, you will need to add your instructor as a collaborator on your fork of the repository to have the ability to add them as a pull request (PR) reviewer. You should push your changes to a new branch on your fork after finishing each issue. You can then open a pull request to merge your code changes into the main branch of your fork, and request review by your instructor. After your instructor approves the pull request, you can merge the PR - make sure to pull those changes to your local copy of the repository after merging. You may then continue on with the next issue.
If you would like to complete this tutorial without instructor support, you can do that as well! You just need to clone a copy of the repository onto your local computer and proceed through each issue. You do not need to open pull requests or ask for review if you are completing this course on your own.