CBIcall

CNAG Biomedical Informatics framework for variant calling

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CBIcall (CNAG Biomedical Informatics framework for variant calling) 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:

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:

cbicall demo

For a configured analysis:

cbicall run -p parameters.yaml -t 4

Citation

CBIcall: a configuration-driven framework for variant calling in large sequencing cohorts. Preprint DOI.

Author

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

License

CBIcall is distributed under the GPLv3 license.

Project links

Data verified by PyPI on Aug 7, 2026
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  • Released:
Newer release available (1.3.0)

1 maintainer

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Avatar for mrueda from gravatar.com mrueda

Credits

Author: Manuel Rueda

GitHub Statistics

Data verified by PyPI on Aug 7, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License expression

GPL-3.0-only
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Requires

Python >=3.8

Provides Extra

all build multiqc snakemake test

Tags

bioinformatics genomics reproducibility variant-calling workflow

Classifiers

Report project as malware

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