BIDS integration into snakemake workflows
Project description
Snakebids
Snakebids is a Python package that extends Snakemake, enabling users to create reproducible, scalable pipelines for processing neuroimaging data in the BIDS format. Snakebids workflows expose a CLI that conforms to the BIDS App guidelines.
Features
Snakebids includes all of the features of Snakemake, including flexible configuration, parallel execution, and Docker/Singularity support, plus:
- Built-in support for BIDS datasets: Seamless workflow functionality with a wide range of BIDS datasets, accomodating various levels of complexity.
- BIDS App Creation: Provide command-line invocations of your workflow following BIDS App guidelines, ensuring reproducibility and enhancing accessibility of your workflow.
- BIDS Path Construction: Easy, flexible construction of valid BIDS paths following BIDS guiding principles, promoting data organization and sharing.
- Plugin System: Extend the functionality of Snakebids by creating and using plugins to meet your workflow's needs.
- Pybids Querying: Leverages Pybids to efficiently retrieve specific data required.
Installation
Snakebids can be installed using pip:
pip install snakebids
Usage
To create and run a Snakebids workflow, you need to:
- Create a Snakefile: Define the steps of your workflow, including input / output files, processing rules, and dependencies
- Create a configuration file: Customize workflow behaviour using a YAML configuration file. Specify input / output directories and custom workflow parameters.
- Run the pipeline: Execute the Snakebids pipeline by invoking the BIDS App CLI or via Snakemake executable.
For detailed instructions and examples, please refer to the documentation.
Contributing
Snakebids is an open-source project, and contributions are welcome! If you have any bug reports, feature requests, or improvements, please submit them to the issues page.
To contribute, first clone the Github repository. Snakebids dependencies are managed with Poetry (version 1.2 or higher). Please refer to the poetry website for installation instructions.
Note: Snakebids makes use of Poetry's dynamic versioning. To see a version number on locally installed Snakebids versions, you will have to also install poetry-dynamic-versioning
plugin to your poetry installation (`poetry self add "poetry-dynamic-versioning[plugin]"). This is not required for contribution.
Following installation of Poetry, the development can be set up by running the following commands:
poetry install
poetry run poe setup
Snakebids uses poethepoet as a task runner. You can see what commands are available by running:
poetry run poe
Tests are done with pytest
and can be run via:
poetry run poe test
Additionally, Snakebids uses pre-commit hooks (installed via the poe setup
command above) to lint and format code (we use black, isort and ruff. By default, these hooks are run on every commit. Please be sure they all pass before making a PR.
License
Snakebids is distributed under the MIT License.
Acknowledgements
Snakebids extends the Snakemake workflow management system and follows the guidelines outlined by the BIDS specification.
Relevant papers
- Mölder F, Jablonski KP, Letcher B et al. Sustainable data analysis with Snakemake [version 2; peer review: 2 approved]. F1000Research. 2021. doi: 10.12688/f1000research.29032.2
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file snakebids-0.13.1.tar.gz
.
File metadata
- Download URL: snakebids-0.13.1.tar.gz
- Upload date:
- Size: 81.1 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: poetry/1.8.3 CPython/3.9.19 Linux/6.5.0-1018-azure
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | 97395a8dfe225e1a15f66dd3562e07afa48370318cba932f0b375f860ff9c2c4 |
|
MD5 | a66236db6c66a7d9ee39549e3e8af9c6 |
|
BLAKE2b-256 | 650e07ec7dcd8de0857833d1ad075c74deed3e00670d3de8c888ce8346f0a805 |
File details
Details for the file snakebids-0.13.1-py3-none-any.whl
.
File metadata
- Download URL: snakebids-0.13.1-py3-none-any.whl
- Upload date:
- Size: 107.0 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: poetry/1.8.3 CPython/3.9.19 Linux/6.5.0-1018-azure
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | 3c68251d54e0615c3bdbf5b8050c0c0a3a58b9789a44c5e1bf75b3ec310cd7a5 |
|
MD5 | dab6eaa28f2c00728e4cac08c924b6f9 |
|
BLAKE2b-256 | 0d89c07e35697c857cfdd610d50d1de27b29ff19732cfd3982c60753293bc8fd |