Metadata-Version: 2.4
Name: cbicall
Version: 1.2.0
Summary: Configuration-driven framework for reproducible variant calling
Project-URL: Homepage, https://cnag-biomedical-informatics.github.io/cbicall/
Project-URL: Documentation, https://cnag-biomedical-informatics.github.io/cbicall/
Project-URL: Repository, https://github.com/CNAG-Biomedical-Informatics/cbicall
Project-URL: Issues, https://github.com/CNAG-Biomedical-Informatics/cbicall/issues
Project-URL: Changelog, https://github.com/CNAG-Biomedical-Informatics/cbicall/blob/main/CHANGELOG.md
Author-email: Manuel Rueda <manuel.rueda@cnag.eu>
License-Expression: GPL-3.0-only
License-File: LICENSE
Keywords: bioinformatics,genomics,reproducibility,variant-calling,workflow
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Requires-Dist: gdown>=5.0
Requires-Dist: jsonschema>=4.18
Requires-Dist: pyyaml>=6.0
Provides-Extra: all
Requires-Dist: multiqc; extra == 'all'
Requires-Dist: pulp==2.6.0; extra == 'all'
Requires-Dist: snakemake; extra == 'all'
Provides-Extra: build
Requires-Dist: build>=1.2; extra == 'build'
Requires-Dist: twine>=5; extra == 'build'
Provides-Extra: multiqc
Requires-Dist: multiqc; extra == 'multiqc'
Provides-Extra: snakemake
Requires-Dist: pulp==2.6.0; extra == 'snakemake'
Requires-Dist: snakemake; extra == 'snakemake'
Provides-Extra: test
Requires-Dist: pytest-cov>=4; extra == 'test'
Requires-Dist: pytest>=7; extra == 'test'
Description-Content-Type: text/markdown

<div align="center">
  <a href="https://github.com/CNAG-Biomedical-Informatics/cbicall">
    <img src="https://raw.githubusercontent.com/CNAG-Biomedical-Informatics/cbicall/main/docs-site/static/img/cbicall-logo.png"
         width="300" alt="CBIcall">
  </a>
  <p><em>CNAG Biomedical Informatics framework for variant calling</em></p>
</div>


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---

**CBIcall** (**C**NAG **B**iomedical **I**nformatics framework for variant **call**ing) is a
configuration-driven framework for running and auditing variant-calling
workflows across heterogeneous computing environments.

Users describe an analysis in one YAML file. CBIcall validates the request,
resolves compatible workflows and resources, launches the selected backend, and
records structured evidence for reproducibility and run comparison. The bundled
workflow collection is identified as `cbicall-core`; selected external nf-core
workflows are also supported.

**Documentation:** <https://cnag-biomedical-informatics.github.io/cbicall/>

## Installation

Install CBIcall from PyPI:

```bash
python3 -m pip install --upgrade cbicall
```

Ready-to-run workflows require additional tools and reference resources. The
documentation covers the resource bundle, optional Python integrations, source
installation, Docker, and Apptainer.

## Quick Start

Generate example WES and mtDNA reports without installing workflow dependencies
or the external resource bundle:

```bash
cbicall demo
```

For a configured analysis:

```bash
cbicall run -p parameters.yaml -t 4
```

## Citation

CBIcall: a configuration-driven framework for variant calling in large sequencing cohorts. [Preprint DOI](https://doi.org/10.64898/2026.03.23.713646).

## Author

Manuel Rueda, PhD. CNAG: <https://www.cnag.eu>

## License

CBIcall is distributed under the
[GPLv3 license](https://github.com/CNAG-Biomedical-Informatics/cbicall/blob/main/LICENSE).
