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 to check that the resource catalog and installed bundle match the workflow you plan 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.

Check the Installation

Run the installation-level check without a parameters YAML:

cbicall doctor

doctor checks the packaged workflow registry and resource catalog, the bundle installed under CBICALL_DATA, and the available workflow backends. Missing optional backends are reported as warnings. The command reads the installation metadata; it does not rehash the large resource archive.

This command verifies the installation as a whole. It does not select a resource for an analysis or determine whether a particular YAML contract can run.

Set the Installed Bundle Location

Bundled workflows read the external resource location from CBICALL_DATA:

export CBICALL_DATA=/absolute/path/to/cbicall-data

The directory should contain Databases/, NGSutils/, and the installation metadata created by cbicall install-resources. The Python driver applies this single value to all native backends; users should not edit packaged env.sh or config.yaml files inside site-packages.

Validate the Catalog

Validate the default catalog:

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	cbicall validate-resources --resource cbicall-germline-resources-v1
nf-core/demo	cbicall validate-resources --resource nf-core-demo-managed-resources-v1
nf-core/Sarek	cbicall validate-resources --resource nf-core-sarek-managed-resources-v1
Custom catalog	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:

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

Runs that reach workflow launch record resource provenance in log.json and run-report.json, including failed executions. Compare repeated runs with:

cbicall compare-runs run_a/ run_b/ --output compare-report.txt

For adding a new resource entry, see Adding Resources.