Tests

Unit tests

Unit tests for the python and R modules used in this workflow can be found in tests/ and run using Pytest and testthat, respectively. Both of which are included in the conda run-time environment for this pipeline.

To run all available python unit tests:

conda activate 54gene-olink-qc
pytest -s tests/*.py

To run all available R unit tests for a particular script:

testthat::test_file("tests/testthat/test-<R script name>.R")

Or to run all available R unit tests:

testthat::test_dir("tests/testthat")

Pipeline/Integration tests

To test the pipeline, we provide a small test dataset and instructions on how to use this dataset available in a repository here.

To summarize, this dataset contains an Olink NPX (Normalized Protein eXpression) dataset containing 23 samples and 2 controls tested for 92 protein biomarkers on a cardiometabolic panel, and the corresponding metadata for each sample in CSV format. The SHA-256 checksum for the dataset that should be normally found is also included.

CI/CD

The aforementioned python and R unit tests and integration tests 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.