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.