Resource Validation
In CBIcall, a resource is the external dependency layer used by workflows: third-party tools, reference genomes, known-sites files, interval lists, and auxiliary databases. A run selects one resource key in the parameters YAML:
resource: cbicall-germline-resources-v1
The resource catalog is the JSON inventory of those resource entries:
resources/cbicall-resource-catalog.json. It records resource type,
resource version, workflow compatibility, and optional identity metadata.
Use this page when the question is: does this resource catalog, selected resource key, or installed resource directory match the workflow I am about to run?
Use Integration Tests when you want to run the shipped example workflows and compare output VCFs.
For the resource model and JSON examples, see Adding Resources. For the current CBIcall-provided bundle, see Bundle v1.
Validate the Catalog
Validate the default catalog:
bin/cbicall validate-resources
This checks the catalog shape and confirms that declared workflow compatibility keys exist.
Validate one resource key or a custom catalog
| Case | Command |
|---|---|
| Native bundle | bin/cbicall validate-resources --resource cbicall-germline-resources-v1 |
| nf-core/demo | bin/cbicall validate-resources --resource nf-core-demo-managed-resources-v1 |
| nf-core/Sarek | bin/cbicall validate-resources --resource nf-core-sarek-managed-resources-v1 |
| Custom catalog | bin/cbicall validate-resources --catalog /path/to/cbicall-resource-catalog.json --resource my-center-germline-v1 |
Validate One Run
Use validate-parameters with the parameters YAML that will be launched:
bin/cbicall validate-parameters -p my-center-wes.yaml
This checks the selected resource against the resolved workflow and
installed resource metadata when present. Bundle resources can be checked
against DATADIR metadata; externally managed resources, such as nf-core/Sarek,
record catalog identity and compatibility but do not use CBIcall bundle
installation checks.
Runtime Provenance
Completed runs record resource provenance in log.json and run-report.json.
Compare repeated runs with:
bin/cbicall compare-runs run_a/ run_b/ --output compare-report.txt
For adding a new resource entry, see Adding Resources.