Quickstart

Use this page to check that CBIcall runs, then choose the workflow family you want to exercise first.

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

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.

1. Confirm the CLI

bin/cbicall --help
bin/cbicall --version

You should see the command help and the installed CBIcall version.

2. Choose a First Test

CBIcall now has two useful first-run paths:

Path	Needs the CBIcall resource bundle?	Use when
nf-core provider	No	You want to test CBIcall orchestration immediately with Nextflow/nf-core.
Native CBIcall WES/mtDNA	Yes	You want to test the bundled Bash/Snakemake/Nextflow/Cromwell workflows against CBIcall's 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.

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

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

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

4. Option B: Run the Native WES Example Test

From the repository root:

bin/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 and configured.

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.

5. Optional: Run the mtDNA Test

Run this after the WES test works:

bin/cbicall test --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.

6. Run With Your Own YAML

Once the integration tests work, use the normal invocation:

bin/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