CNAG Biomedical Informatics framework for variant calling
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
Rueda M, Fernandez-Orth D, Gut IG. CBIcall: a configuration-driven framework for variant calling in large sequencing cohorts. Bioinformatics Advances. 2026. doi:10.1093/bioadv/vbag232.
Author
Manuel Rueda, PhD. CNAG: https://www.cnag.eu
License
CBIcall is distributed under the GPLv3 license.
1 maintainer
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