Tests
Unit tests
Unit tests for the python modules used in this workflow can be found in workflow/scripts/tests
and run using Pytest which is included in the conda run-time environment for this pipeline.
To run all available unit tests:
conda activate 54gene-wgs-germline
pytest -s workflow/scripts/tests/*.py
Pipeline/Integration tests
To test the core pipeline, we provide a small test dataset and instructions on how to use this dataset available in a repository here.
To summarize, this test dataset contains a small region of chromosome 21 from the NA12878 platinum reference genome. The above repository contains all necessary inputs (configuration file, manifest, intervals, sex_linker files) required to run the pipeline in all three run-modes. The README provides instructions on how to use these files to execute a test using the 54gene-wgs-germline pipeline.
Snakemake unit tests
In development (TBD)
CI/CD
The aforementioned python unit tests and integration tests (in all three run-modes) are run as part of the Gitlab Continuous Integration (CI) pipeline for this codebase. You can find the status of the CI pipeline on the main repository page.
Note: The test suite and CI pipeline are still a work in progress.