Quickstart
Use this page to check that CBIcall runs on the shipped example data, then run your own YAML file.
If you still need to choose an installation method or workflow, start with the Overview.
1. Confirm the CLI
bin/cbicall --help
bin/cbicall --version
You should see the command help and the installed CBIcall version.
2. Run the WES Example Test
From the repository root:
bin/cbicall test --wes -t 1
This runs the bundled WES example and compares the generated VCF with the shipped reference output.
Use Integration Tests for bundled WES/mtDNA test details,
Configuration Reference for
validate-param, and Resource Validation for resource
catalog checks.
3. Optional: Run the mtDNA Test
Run this after the WES test works:
bin/cbicall test --mit -t 1
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.
4. 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 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 |