Quickstart

Use this page to inspect CBIcall's reports immediately, then choose the workflow family you want to execute first.

If you still need to choose an installation method or workflow, start with the Overview.

1. Install from PyPI

python3 -m pip install --upgrade cbicall

Install optional Snakemake and MultiQC integrations with python3 -m pip install --upgrade "cbicall[all]". Container and source installation alternatives are described under Install.

YAML contract

In CBIcall, the parameters YAML becomes a YAML contract after CBIcall has validated it and resolved it against the workflow registry and resource catalog. Both validate-parameters and run perform this validation; validate-parameters stops before launching the workflow.

2. Confirm the CLI

cbicall --help
cbicall --version
cbicall doctor

You should see the command help, the installed CBIcall version, and a concise installation report. doctor checks the packaged contracts, CBICALL_DATA bundle metadata, and available workflow backends. Missing optional backends are reported as warnings.

3. Explore the Reports

Generate a WES audit report and an interactive mtDNA browser from packaged example outputs:

cbicall demo

CBIcall writes both reports under cbicall-demo/ and prints their paths. This command needs no external resource bundle, workflow backend, Java installation, or container runtime.

Precomputed demonstration

The demo uses sanitized, precomputed outputs from the packaged CNAG99901P integration fixture. It exercises CBIcall's reporting code but does not execute BWA, GATK, or MToolBox, and it is not an analytical benchmark.

Use a different empty destination when needed:

cbicall demo --output-dir my-cbicall-demo

4. Choose an Execution Test

For actual workflow execution, choose one of these paths:

Path	CBIcall bundle	Other requirements	Use when
nf-core provider	No	Nextflow and the selected container runtime	You want to test external-provider orchestration.
Native CBIcall WES/mtDNA	Yes	Tools supplied by the bundle	You want to execute packaged native workflows against CBIcall integration contracts.

For nf-core, CBIcall validates the YAML and records provenance, while nf-core and Nextflow manage the workflow's own test data, containers, and references.

5. Option A: Run nf-core Without the CBIcall Bundle

From examples/input, run the lightweight nf-core demo example:

cd examples/input
cbicall validate-parameters -p nf-core-demo.yaml --no-color
cbicall run -p nf-core-demo.yaml -t 4 --no-color

This does not require the CBIcall germline resource bundle or DATADIR. It does require Nextflow and the container/runtime profile selected in the YAML, for example test,singularity on HPC or test,docker on a Docker workstation.

6. Option B: Run the Native WES Example Test

Point CBIcall to the installed external bundle, then run the test:

export CBICALL_DATA=/absolute/path/to/cbicall-data
cbicall test --wes-bash -t 1

This runs the bundled Bash WES workflow and validates the generated VCF against the expected normalized hash declared by the integration contract. It requires the CBIcall-provided resource bundle to be installed. CBICALL_DATA is applied consistently to the Bash, Snakemake, Nextflow, and Cromwell native backends.

Need deeper checks?

Use Integration Tests for bundled WES/mtDNA test details, Configuration Reference for validate-parameters, and Resource Validation for checking the selected resource entry.

7. Optional: Run the mtDNA Test

Run the WES and mtDNA integration contracts together so that the WES test produces the BAM consumed by MToolBox:

cbicall test --wes-bash --mit-bash -t 1

Architecture

The mtDNA workflow uses MToolBox and is x86_64-only. If you are on ARM / aarch64, run WES/WGS workflows there but move mtDNA runs to an x86_64 host.

8. Run With Your Own YAML

Once the integration tests work, use the normal invocation:

cbicall run -p parameters.yaml -t 4

Option	Meaning
-p	YAML parameters file.
-t	Threads passed to the workflow.

For most WES/WGS runs, start with 4 threads and adjust after checking Performance.

Next Steps

Goal	Page
Run nf-core workflows	nf-core Provider
Run real WES/WGS data	End-to-end Example: WES
Run mtDNA analysis	End-to-end Example: mtDNA
Check reproducibility	Run Comparison
Understand generated files	Outputs