Integration Tests

CBIcall ships small integration tests that run the bundled example workflows and compare their outputs against shipped references.

They do not replace biological or clinical validation of the underlying variant-calling methods.

Use this page when the question is: can this CBIcall installation run the shipped example workflows and reproduce the expected example outputs?

This page is about execution tests. If the question is whether a parameters YAML resolves before launch, use validate-param as described in Configuration Reference. If the question is whether a custom resource catalog or installed resource directory is valid, use Resource Validation.

Minimal Test

From the repository root:

bin/cbicall test --wes -t 1

Check	What it confirms
test --wes	The bundled WES workflow runs and reproduces the shipped reference VCF under deterministic comparison rules.

Where to go next

Use this page to run the shipped examples. For parameter-file checks, see Configuration Reference. For comparing repeated runs, see Run Comparison.

Test Commands

bin/cbicall test --wes -t 1
bin/cbicall test --mit -t 1
bin/cbicall test --all -t 1

Command	Use
bin/cbicall test --wes -t 1	Fast WES integration test. Run this first.
bin/cbicall test --mit -t 1	mtDNA integration test after the WES path is working.
bin/cbicall test --all -t 1	Run all bundled integration examples.

Outputs

The test command prints the run directory, workflow log, run-report.json, launcher log, and output file used for comparison.

For WES, the run directory looks like:

CNAG999_exome/CNAG99901P_ex/cbicall_bash_wes_single_b37_gatk-4.6_*/
  01_bam/
  02_varcall/
  03_stats/
  logs/

For mtDNA, the run directory looks like:

CNAG999_exome/CNAG99901P_ex/cbicall_bash_mit_single_rsrs_gatk-3.5_*/
  01_mtoolbox/
  02_browser/

Use Run Comparison when you want to compare two or more completed runs.