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align=\"center\"\u003e\n  \u003ca href=\"https://github.com/mrueda/cbicall\"\u003e\n    \u003cimg src=\"https://raw.githubusercontent.com/CNAG-Biomedical-Informatics/cbicall/main/docs-site/static/img/cbicall-logo.png\"\n         width=\"300\" alt=\"CBIcall\"\u003e\n  \u003c/a\u003e\n  \u003cp\u003e\u003cem\u003eCNAG Biomedical Informatics framework for variant calling\u003c/em\u003e\u003c/p\u003e\n\u003c/div\u003e\n\n\n[![Build](https://github.com/cnag-biomedical-informatics/cbicall/actions/workflows/build-and-test.yml/badge.svg)](https://github.com/cnag-biomedical-informatics/cbicall/actions/workflows/build-and-test.yml)\n![version](https://img.shields.io/badge/version-1.0.1--beta.1-28a745)\n[![Coverage Status](https://coveralls.io/repos/github/CNAG-Biomedical-Informatics/cbicall/badge.svg?branch=main)](https://coveralls.io/github/CNAG-Biomedical-Informatics/cbicall?branch=main)\n[![Docker Build](https://github.com/cnag-biomedical-informatics/cbicall/actions/workflows/docker-build-multi-arch.yml/badge.svg?branch=main)](https://github.com/cnag-biomedical-informatics/cbicall/actions/workflows/docker-build-multi-arch.yml)\n[![Docker Image Size](https://img.shields.io/docker/image-size/manuelrueda/cbicall/latest?logo=docker\u0026label=image%20size)](https://hub.docker.com/r/manuelrueda/cbicall/)\n[![Docker Pulls](https://img.shields.io/docker/pulls/manuelrueda/cbicall.svg?logo=docker\u0026label=pulls)](https://hub.docker.com/r/manuelrueda/cbicall/)\n[![Documentation Status](https://github.com/cnag-biomedical-informatics/cbicall/actions/workflows/documentation.yml/badge.svg)](https://github.com/cnag-biomedical-informatics/cbicall/actions/workflows/documentation.yml)\n[![License](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n\n---\n\n**CBIcall** (**C**NAG **B**iomedical **I**nformatics framework for variant **call**ing) is a\n**configuration-driven framework** for reproducible variant calling in large sequencing cohorts.\nIt validates analysis intent, resolves approved workflow backends and resource definitions,\nand records **structured run reports** for auditable production runs and run-to-run comparison.\n\n**📘 Documentation:** \u003ca href=\"https://cnag-biomedical-informatics.github.io/cbicall\" target=\"_blank\"\u003ehttps://cnag-biomedical-informatics.github.io/cbicall\u003c/a\u003e\n\n**🐳 Docker Hub Image:** \u003ca href=\"https://hub.docker.com/r/manuelrueda/cbicall/tags\" target=\"_blank\"\u003ehttps://hub.docker.com/r/manuelrueda/cbicall/tags\u003c/a\u003e\n\n\n# Table of contents\n- [Installation](#installation)\n  - [Non-Containerized](non-containerized/README.md)\n  - Containerized\n    - [Docker](docker/README.md)\n    - [Apptainer](apptainer/README.md)\n- [Quick Start](#quick-start)\n- [Documentation](#documentation)\n- [Citation](#citation)\n  - [Author](#author)\n- [License](#copyright-and-license)\n\n\nCBIcall orchestrates germline variant calling workflows for Illumina sequencing data.\nIt does **not** implement variant calling algorithms itself. Instead, it validates\nparameters, resolves workflows from a versioned registry, checks resource compatibility,\nlaunches native CBIcall workflows through **Bash, Snakemake, Nextflow, or Cromwell**\nbackends, and captures audit artifacts for traceability. Selected external nf-core\nworkflows can also run through the same validation and provenance layer.\n\nCBIcall uses a three-part execution contract:\n\n| Contract layer | Purpose |\n| --- | --- |\n| Parameters YAML | User analysis intent: inputs, pipeline, mode, genome, backend, and runtime options. |\n| Workflow registry | Approved workflow implementations and backend-specific entrypoints. |\n| Resource catalog | External references, tool/resource bundles, compatibility rules, and resource identity. |\n\nKey points:\n\n- Configuration-driven execution from a YAML parameter file\n- Native CBIcall workflow support through Bash, Snakemake, Nextflow, and Cromwell backends\n- Support for WES, WGS, and mtDNA analysis modes\n- Registry-backed support for selected external nf-core/Nextflow workflows\n- Structured audit artifacts: `log.json`, `run-report.json`, optional `run-report.html`, workflow fingerprints, resource identity, output inventories, and normalized VCF hashes\n- Programmatic run comparison with `cbicall compare-runs`\n- Optional partial workflow starts for supported backends\n\nWorkflow sources:\n\n| Source | Role |\n| --- | --- |\n| Native CBIcall workflows | Packaged WES/WGS/mtDNA pipelines with CBIcall validation, logging, and output structure. |\n| External nf-core workflows | Selected registry-backed Nextflow workflows executed with CBIcall validation and provenance. |\n\n# Quick Start\n\n    bin/cbicall run -p params.yaml -t 8\n\nRunnable examples and sample inputs are available under `examples/`.\n\n# Documentation\n\nThe full technical reference lives in the documentation site and repository docs:\n\n- General usage and parameter reference: [docs-site/docs/usage/usage.md](docs-site/docs/usage/usage.md)\n- Quick start: [docs-site/docs/usage/quickstart.md](docs-site/docs/usage/quickstart.md)\n- 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)\n- Run comparison and audit reports: [docs-site/docs/usage/run-comparison.md](docs-site/docs/usage/run-comparison.md)\n- Technical details: [docs-site/docs/technical-details/architecture.md](docs-site/docs/technical-details/architecture.md)\n\n# Citation\n\nCBIcall: a configuration-driven framework for variant calling in large sequencing cohorts. [Preprint DOI](https://doi.org/10.64898/2026.03.23.713646).\n\n# Author\n\nWritten by Manuel Rueda (mrueda). GitHub repository: [https://github.com/CNAG-Biomedical-Informatics/cbicall](https://github.com/CNAG-Biomedical-Informatics/cbicall).\n\n# Copyright and license\n\nPlease see the included LICENSE file for distribution and usage terms.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcnag-biomedical-informatics%2Fcbicall","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcnag-biomedical-informatics%2Fcbicall","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcnag-biomedical-informatics%2Fcbicall/lists"}