https://github.com/cnag-biomedical-informatics/cbicall
CBIcall is a configuration-driven framework for reproducible variant calling in large sequencing cohorts, enabling standardized pipelines from FASTQ to analysis-ready VCFs across heterogeneous computing environments.
https://github.com/cnag-biomedical-informatics/cbicall
bash bioinformatics bioinformatics-tool genomics germline-variant-calling json-schema nextflow nextflow-pipeline ngs ngs-analysis ngs-pipeline python snakemake snakemake-pipeline variant-calling
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CBIcall is a configuration-driven framework for reproducible variant calling in large sequencing cohorts, enabling standardized pipelines from FASTQ to analysis-ready VCFs across heterogeneous computing environments.
- Host: GitHub
- URL: https://github.com/cnag-biomedical-informatics/cbicall
- Owner: CNAG-Biomedical-Informatics
- License: gpl-3.0
- Created: 2025-03-14T06:34:15.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2026-06-26T11:02:47.000Z (7 days ago)
- Last Synced: 2026-06-26T11:10:41.148Z (7 days ago)
- Topics: bash, bioinformatics, bioinformatics-tool, genomics, germline-variant-calling, json-schema, nextflow, nextflow-pipeline, ngs, ngs-analysis, ngs-pipeline, python, snakemake, snakemake-pipeline, variant-calling
- Language: Python
- Homepage: https://cnag-biomedical-informatics.github.io/cbicall/
- Size: 36.1 MB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: Changes
- License: LICENSE
Awesome Lists containing this project
README
CNAG Biomedical Informatics framework for variant calling
[](https://github.com/cnag-biomedical-informatics/cbicall/actions/workflows/build-and-test.yml)
[](https://coveralls.io/github/CNAG-Biomedical-Informatics/cbicall?branch=main)
[](https://github.com/cnag-biomedical-informatics/cbicall/actions/workflows/docker-build-multi-arch.yml)
[](https://hub.docker.com/r/manuelrueda/cbicall/)
[](https://hub.docker.com/r/manuelrueda/cbicall/)
[](https://github.com/cnag-biomedical-informatics/cbicall/actions/workflows/documentation.yml)
[](https://www.gnu.org/licenses/gpl-3.0)
---
**CBIcall** (**C**NAG **B**iomedical **I**nformatics framework for variant **call**ing) 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
# Table of contents
- [Installation](#installation)
- [Non-Containerized](non-containerized/README.md)
- Containerized
- [Docker](docker/README.md)
- [Apptainer](apptainer/README.md)
- [Quick Start](#quick-start)
- [Documentation](#documentation)
- [Citation](#citation)
- [Author](#author)
- [License](#copyright-and-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:
| Contract layer | Purpose |
| --- | --- |
| Parameters YAML | User analysis intent: inputs, pipeline, mode, genome, backend, and runtime options. |
| Workflow registry | Approved workflow implementations and backend-specific entrypoints. |
| Resource catalog | External references, tool/resource bundles, compatibility rules, and resource identity. |
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:
| 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. |
# Quick Start
bin/cbicall run -p params.yaml -t 8
Runnable examples and sample inputs are available under `examples/`.
# Documentation
The full technical reference lives in the documentation site and repository docs:
- General usage and parameter reference: [docs-site/docs/usage/usage.md](docs-site/docs/usage/usage.md)
- Quick start: [docs-site/docs/usage/quickstart.md](docs-site/docs/usage/quickstart.md)
- End-to-end examples: [WES/WGS](docs-site/docs/usage/end-to-end-example-wes.md), [mtDNA](docs-site/docs/usage/end-to-end-example-mit.md)
- Run comparison and audit reports: [docs-site/docs/usage/run-comparison.md](docs-site/docs/usage/run-comparison.md)
- Technical details: [docs-site/docs/technical-details/architecture.md](docs-site/docs/technical-details/architecture.md)
# Citation
CBIcall: a configuration-driven framework for variant calling in large sequencing cohorts. [Preprint DOI](https://doi.org/10.64898/2026.03.23.713646).
# Author
Written by Manuel Rueda (mrueda). GitHub repository: [https://github.com/CNAG-Biomedical-Informatics/cbicall](https://github.com/CNAG-Biomedical-Informatics/cbicall).
# Copyright and license
Please see the included LICENSE file for distribution and usage terms.