CNAG Biomedical Informatics framework for variant calling

CBIcall (CNAG Biomedical Informatics framework for variant calling) is a configuration-driven framework for reproducible variant calling in large sequencing cohorts. It validates analysis intent, resolves approved workflow backends and resource definitions, and records structured run reports for auditable production runs and run-to-run comparison.

📘 Documentation: https://cnag-biomedical-informatics.github.io/cbicall

🐳 Docker Hub Image: https://hub.docker.com/r/manuelrueda/cbicall/tags

• Installation
  • Non-Containerized
  • Containerized
    • Docker
    • Apptainer
• Quick Start
• Documentation
• Citation
  • Author
• License

CBIcall orchestrates germline variant calling workflows for Illumina sequencing data. It does not implement variant calling algorithms itself. Instead, it validates parameters, resolves workflows from a versioned registry, checks resource compatibility, launches native CBIcall workflows through Bash, Snakemake, Nextflow, or Cromwell backends, and captures audit artifacts for traceability. Selected external nf-core workflows can also run through the same validation and provenance layer.

CBIcall uses a three-part execution contract:

Key points:

• Configuration-driven execution from a YAML parameter file
• Native CBIcall workflow support through Bash, Snakemake, Nextflow, and Cromwell backends
• Support for WES, WGS, and mtDNA analysis modes
• Registry-backed support for selected external nf-core/Nextflow workflows
• Structured audit artifacts: log.json, run-report.json, optional run-report.html, workflow fingerprints, resource identity, output inventories, and normalized VCF hashes
• Programmatic run comparison with cbicall compare-runs
• Optional partial workflow starts for supported backends

Workflow sources:

bin/cbicall run -p params.yaml -t 8

Runnable examples and sample inputs are available under examples/.

The full technical reference lives in the documentation site and repository docs:

• General usage and parameter reference: docs-site/docs/usage/usage.md
• Quick start: docs-site/docs/usage/quickstart.md
• End-to-end examples: WES/WGS, mtDNA
• Run comparison and audit reports: docs-site/docs/usage/run-comparison.md
• Technical details: docs-site/docs/technical-details/architecture.md

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

Written by Manuel Rueda (mrueda). GitHub repository: https://github.com/CNAG-Biomedical-Informatics/cbicall.

Please see the included LICENSE file for distribution and usage terms.