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 records structured provenance for auditable production runs.
📘 Documentation: https://cnag-biomedical-informatics.github.io/cbicall
🐳 Docker Hub Image: https://hub.docker.com/r/manuelrueda/cbicall/tags
- Installation
- Non-Containerized
- Containerized
- Quick Start
- Documentation
- Citation
- 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, launches native CBIcall workflows through Bash, Snakemake, Nextflow, or Cromwell backends, and captures logs, run reports, output fingerprints, and structured metadata for traceability. Selected external nf-core workflows can also run through the same validation and provenance layer.
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 run logging and traceable runtime metadata
- Optional partial workflow starts for supported backends
Workflow sources:
| Source | Role |
|---|---|
| Native CBIcall workflows | Packaged WES/WGS/mtDNA pipelines with CBIcall validation, logging, and output structure. |
| External nf-core workflows | Selected registry-backed Nextflow workflows executed with CBIcall validation and provenance. |
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/usage/usage.md
- Quick start: docs/usage/quickstart.md
- End-to-end examples: docs/usage/end-to-end-example-wes.md, docs/usage/end-to-end-example-mit.md
- Technical details: 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.