snakemake
This is the development home of the workflow management system Snakemake. For general information, see
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
55 of 375 committers (14.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.6%) to scientific vocabulary
Keywords
reproducibility
snakemake
workflow-management
Keywords from Contributors
bioinformatics
genomics
closember
pypi
lesson
reporting
dna
workflow-engine
sequence-alignment
quality-control
Last synced: 6 months ago
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JSON representation
Repository
This is the development home of the workflow management system Snakemake. For general information, see
Basic Info
- Host: GitHub
- Owner: snakemake
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://snakemake.github.io
- Size: 90.6 MB
Statistics
- Stars: 2,563
- Watchers: 18
- Forks: 605
- Open Issues: 1,210
- Releases: 318
Topics
reproducibility
snakemake
workflow-management
Created over 6 years ago
· Last pushed 6 months ago
Metadata Files
Readme
Changelog
License
Code of conduct
Codeowners
README.md
Snakemake
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Snakemake is highly popular, with on average more than 7 new citations per week in 2021, and almost 400k downloads. 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.
Homepage: https://snakemake.github.io
Copyright (c) 2012-2022 Johannes Köster johannes.koester@uni-due.com (see LICENSE)
Owner
- Name: Snakemake
- Login: snakemake
- Kind: organization
- Website: https://snakemake.github.io
- Twitter: johanneskoester
- Repositories: 12
- Profile: https://github.com/snakemake
GitHub Events
Total
- Create event: 159
- Commit comment event: 2
- Release event: 18
- Issues event: 327
- Watch event: 274
- Delete event: 167
- Issue comment event: 2,205
- Push event: 730
- Pull request event: 540
- Pull request review comment event: 509
- Pull request review event: 959
- Fork event: 67
Last Year
- Create event: 159
- Commit comment event: 2
- Release event: 18
- Issues event: 328
- Watch event: 274
- Delete event: 168
- Issue comment event: 2,209
- Push event: 733
- Pull request event: 543
- Pull request review comment event: 512
- Pull request review event: 963
- Fork event: 67
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Johannes Köster | j****r@t****e | 3,062 |
| johannes.koester@gmail.com | j****r@g****m@9****5 | 398 |
| github-actions[bot] | 4****] | 206 |
| Christopher Tomkins-Tinch | t****c@b****g | 76 |
| Per Unneberg | p****g@s****e | 60 |
| Rasmus Ågren | r****n@s****e | 52 |
| Tim Booth | t****h@e****k | 44 |
| Oliver Stolpe | o****e@b****e | 41 |
| Vanessasaurus | v****t@s****u | 37 |
| snakemake-bot | s****n@g****m | 35 |
| Filipe G. Vieira | 1****a | 32 |
| johannes.koester@googlemail.com | j****r@g****m@9****5 | 30 |
| David Laehnemann | d****n@h****e | 28 |
| Henning Timm | h****m@t****e | 27 |
| Christopher Burr | c****r@c****h | 25 |
| David Koppstein | d****n@a****m | 24 |
| Manuel Holtgrewe | m****e@b****e | 23 |
| dependabot[bot] | 4****] | 23 |
| Michael Hall | m****l@m****h | 19 |
| Marcel Martin | m****n@s****e | 18 |
| Cade Mirchandani | c****n@u****u | 17 |
| Ryan C. Thompson | r****t@t****g | 16 |
| Hocnonsense | 4****e | 15 |
| Felix Mölder | f****r@u****e | 15 |
| Morten Enemark Lund | m****d@g****m | 15 |
| bow | b****w@b****d | 13 |
| Simon Ye | s****7@g****m | 13 |
| Peter Van Dyken | 8****n | 13 |
| Ben Beasley | c****e@m****t | 13 |
| Elmar Pruesse | e****e | 12 |
| and 345 more... | ||
Committer Domains (Top 20 + Academic)
cern.ch: 8
tu-dortmund.de: 7
scilifelab.se: 3
bihealth.de: 3
ucdavis.edu: 2
gmx.de: 2
posteo.de: 2
stanford.edu: 2
wustl.edu: 2
env.ethz.ch: 1
kyleam.com: 1
pacificbiosciences.com: 1
brueffer.io: 1
esok.(none): 1
biogen.com: 1
zoho.com: 1
princeton.edu: 1
cs.uni-saarland.de: 1
tbdwebdesign.nl: 1
txbiomed.org: 1
luc.edu: 1
ucl.ac.uk: 1
imtek.uni-freiburg.de: 1
udo.edu: 1
cpr.ku.dk: 1
iiitd.ac.in: 1
ebi.ac.uk: 1
broadinstitute.org: 1
ed.ac.uk: 1
ucsc.edu: 1
uni-due.de: 1
niddk.nih.gov: 1
jimmy.harvard.edu: 1
gis.a-star.edu.sg: 1
tudelft.nl: 1
wmc07-f52.broadinstitute.org: 1
usys.ethz.ch: 1
cornell.edu: 1
molgen.mpg.de: 1
uni-jena.de: 1
roslin.ed.ac.uk: 1
ucla.edu: 1
cs.ubc.ca: 1
ucsd.edu: 1
cruk.manchester.ac.uk: 1
ifu.baug.ethz.ch: 1
lt5.binf.ku.dk: 1
kit.edu: 1
case.edu: 1
manchester.ac.uk: 1
iupui.edu: 1
berkeley.edu: 1
uw.edu: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 802
- Total pull requests: 1,284
- Average time to close issues: 8 months
- Average time to close pull requests: about 1 month
- Total issue authors: 475
- Total pull request authors: 185
- Average comments per issue: 2.47
- Average comments per pull request: 2.29
- Merged pull requests: 892
- Bot issues: 3
- Bot pull requests: 215
Past Year
- Issues: 236
- Pull requests: 598
- Average time to close issues: 22 days
- Average time to close pull requests: 7 days
- Issue authors: 156
- Pull request authors: 87
- Average comments per issue: 1.11
- Average comments per pull request: 1.93
- Merged pull requests: 405
- Bot issues: 3
- Bot pull requests: 59
Top Authors
Issue Authors
- johanneskoester (19)
- fgvieira (16)
- pdimens (14)
- corneliusroemer (14)
- lczech (12)
- irm-codebase (9)
- vsoch (8)
- Redmar-van-den-Berg (8)
- cademirch (8)
- peterjc (8)
- hermidalc (7)
- cmeesters (6)
- MuhammadRohanA (6)
- dlaehnemann (6)
- gipert (5)
Pull Request Authors
- johanneskoester (367)
- github-actions[bot] (183)
- fgvieira (58)
- snakemake-bot (53)
- Hocnonsense (37)
- cademirch (35)
- dependabot[bot] (30)
- musicinmybrain (23)
- jjjermiah (22)
- cmeesters (22)
- jakevc (16)
- laf070810 (15)
- dlaehnemann (14)
- fxwiegand (14)
- vsoch (10)
Top Labels
Issue Labels
bug (463)
enhancement (246)
stale (44)
hackathon-2025 (7)
documentation (4)
help wanted (3)
question (3)
needs example (1)
good first issue (1)
autorelease: pending (1)
awaiting-test-with-latest-release (1)
Pull Request Labels
autorelease: tagged (121)
autorelease: pending (115)
dependencies (30)
github_actions (14)
bug (12)
documentation (11)
hackathon-2025 (9)
enhancement (7)
stale (6)
WIP (4)
update-container-image (2)
help wanted (1)
Packages
- Total packages: 1
-
Total downloads:
- pypi 115,488 last-month
- Total docker downloads: 2,879,480
- Total dependent packages: 81
- Total dependent repositories: 547
- Total versions: 420
- Total maintainers: 1
pypi.org: snakemake
Workflow management system to create reproducible and scalable data analyses
- Homepage: https://snakemake.github.io
- Documentation: https://snakemake.readthedocs.io
- License: mit
-
Latest release: 9.11.1
published 6 months ago
Rankings
Dependent packages count: 0.3%
Dependent repos count: 0.6%
Docker downloads count: 0.8%
Downloads: 1.0%
Average: 1.1%
Stargazers count: 1.6%
Forks count: 2.5%
Maintainers (1)
Last synced:
6 months ago
Dependencies
.github/workflows/conventional-prs.yml
actions
- amannn/action-semantic-pull-request v5.0.2 composite
.github/workflows/docker-publish.yml
actions
- actions/checkout v4 composite
- docker/setup-buildx-action v2 composite
- elgohr/Publish-Docker-Github-Action v5 composite
.github/workflows/main.yml
actions
- actions/checkout v4 composite
- actions/checkout v3 composite
- mamba-org/setup-micromamba v1 composite
- marocchino/sticky-pull-request-comment v2.8.0 composite
- vegardit/fast-apt-mirror.sh 1.0.0 composite
.github/workflows/release-please.yml
actions
- GoogleCloudPlatform/release-please-action v3 composite
- actions/checkout v3 composite
- actions/setup-python v4 composite
- elgohr/Publish-Docker-Github-Action v5 composite
- pypa/gh-action-pypi-publish release/v1 composite
Dockerfile
docker
- mambaorg/micromamba latest build
examples/flux/Dockerfile
docker
- fluxrm/flux-sched focal build
tests/test_containerized/Dockerfile
docker
- condaforge/mambaforge latest build
tests/test_remote_irods/Dockerfile
docker
- "mjstealey/irods-provider-postgres 4.2.2" build
docs/requirements.txt
pypi
- appdirs *
- configargparse *
- docutils *
- myst-parser *
- snakemake-interface-common *
- snakemake-interface-executor-plugins *
- snakemake-interface-storage-plugins *
- sphinx >=3
- sphinx-argparse *
- sphinxcontrib-napoleon *
pyproject.toml
pypi
setup.py
pypi
tests/test_prebuilt_conda_script/dummy_package/pyproject.toml
pypi
tests/test_get_log_both/environment.yaml
conda
tests/test_get_log_complex/environment.yaml
conda
tests/test_get_log_none/environment.yaml
conda
tests/test_get_log_stderr/environment.yaml
conda
tests/test_get_log_stdout/environment.yaml
conda
tests/test_issue1046/my_wrapper/environment.yaml
conda
tests/test_r_wrapper/environment.yaml
conda
tests/test_subworkflow_config/environment.yml
conda