CBIcall¶
Reproducible germline variant calling for Illumina DNA sequencing
What is CBIcall?¶
CBIcall (CNAG Biomedical Informatics framework for variant calling) is a framework for running Illumina-based germline variant calling workflows using curated Bash and Snakemake pipelines.
The system provides a command-line interface, a validated YAML configuration, and a registry-driven dispatcher that ensures only supported workflows are executed.
Core functionality¶
CBIcall is a workflow orchestrator: it runs predefined pipelines but does not re-implement bioinformatics tools.
It performs the following tasks:
- Validates user parameters and compatibility (engine, GATK version, genome, mode)
- Loads a versioned workflow registry (YAML) validated with JSON Schema
- Resolves workflow scripts and checks that referenced files exist and are executable
- Creates a per-run project directory with a unique run identifier
- Executes the selected workflow and captures stdout/stderr into a unified log file
All biological processing is performed by external tools and workflows (e.g. BWA, GATK, MToolBox).
Supported pipelines¶
| Pipeline | Mode | Genome | GATK version | Status / Notes |
|---|---|---|---|---|
| WES | single |
b37 (default) |
gatk-3.5, gatk-4.6 |
✓ Supported |
| WES | cohort |
b37 (default) |
gatk-3.5, gatk-4.6 |
✓ Supported |
| WGS | single |
b37 (default), hg38 |
gatk-4.6 |
✓ Supported |
| WGS | cohort |
b37 (default), hg38 |
gatk-4.6 |
✓ Supported |
| MIT (mtDNA) | single |
rsrs (fixed) |
gatk-3.5 |
⚠ Not supported on ARM / aarch64 |
| MIT (mtDNA) | cohort |
rsrs (fixed) |
gatk-3.5 |
⚠ Not supported on ARM / aarch64 |
✓ Fully supported configuration ⚠ Platform limitation
Date: March-2026
Workflow engines¶
CBIcall dispatches workflows declared in an external registry:
- Bash (fully supported)
- Snakemake (supported with GATK ≥ 4.6)
- Nextflow (declared but not implemented)
Workflow resolution order: engine → GATK version → pipeline → mode
Only workflows declared in the registry and present on disk with executable permissions can be executed.
Configuration philosophy¶
CBIcall uses a single YAML parameter file with:
- Explicit defaults
- Strict enum validation
- Fail-fast semantic checks (e.g. incompatible genome/pipeline combinations)
- Limited parameter inference where appropriate (e.g. default genome selection)
This design helps detect configuration errors before workflow execution.
Reproducibility and traceability¶
For every run, CBIcall:
- Generates a unique run identifier
- Creates a dedicated project directory
- Writes a structured
log.jsoncontaining:- CLI arguments
- Resolved configuration
- User parameters
- Captures the workflow stdout/stderr into a single log file
These records allow runs to be inspected, reproduced, and debugged.