snakemake-novice-bioinformatics
Introduction to Snakemake for Bioinformatics
https://github.com/carpentries-incubator/snakemake-novice-bioinformatics
Science Score: 54.0%
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3 of 8 committers (37.5%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (14.8%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Introduction to Snakemake for Bioinformatics
Basic Info
- Host: GitHub
- Owner: carpentries-incubator
- License: other
- Language: Python
- Default Branch: main
- Homepage: https://carpentries-incubator.github.io/snakemake-novice-bioinformatics
- Size: 12 MB
Statistics
- Stars: 20
- Watchers: 5
- Forks: 9
- Open Issues: 20
- Releases: 0
Topics
Metadata Files
README.md
Snakemake for Bioinformatics
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.
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
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 
. 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
Owner
- Name: carpentries-incubator
- Login: carpentries-incubator
- Kind: organization
- Repositories: 107
- Profile: https://github.com/carpentries-incubator
Citation (CITATION)
https://edcarp.github.io/Ed-DaSH/workshops.html
GitHub Events
Total
- Issues event: 4
- Watch event: 3
- Issue comment event: 5
- Push event: 59
- Pull request event: 1
Last Year
- Issues event: 4
- Watch event: 3
- Issue comment event: 5
- Push event: 59
- Pull request event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Tim Booth | t****h@e****k | 185 |
| Lex Nederbragt | l****t@i****o | 2 |
| John Blischak | j****k@g****m | 2 |
| Ezra Herman | 5****n | 2 |
| Zhian N. Kamvar | z****r@g****m | 1 |
| Toby Hodges | t****s@g****m | 1 |
| Edward Wallace | e****e | 1 |
| ameynert | a****t@i****k | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 95
- Total pull requests: 19
- Average time to close issues: about 2 months
- Average time to close pull requests: about 1 month
- Total issue authors: 6
- Total pull request authors: 7
- Average comments per issue: 1.98
- Average comments per pull request: 0.84
- Merged pull requests: 14
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 33
- Pull requests: 4
- Average time to close issues: about 1 month
- Average time to close pull requests: 4 months
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 1.52
- Average comments per pull request: 1.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- tbooth (36)
- ezherman (14)
- lexnederbragt (5)
- ewallace (1)
- mwhamgenomics (1)
- tly0505 (1)
Pull Request Authors
- carpentries-bot (6)
- lexnederbragt (3)
- jdblischak (2)
- ezherman (1)
- ameynert (1)
- ewallace (1)
- zkamvar (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/cache v1 composite
- actions/checkout master composite
- actions/setup-python v2 composite
- actions/setup-ruby main composite
- r-lib/actions/setup-r v2 composite
- actions/cache v1 composite
- actions/checkout master composite
- actions/setup-python v2 composite
- actions/setup-ruby v1 composite
- r-lib/actions/setup-r v2 composite
- github-pages >= 0 development