Testing

This section provides intructions to run unit and integration tests to ensure a proper functioning of the workflow. These tests can be further used as a validation step upon any changes to the workflow.

Running the tests

The following command executes unit tests, one for each rule in the workflow. An integration test is also configured to run with a small real-world dataset from Zackular et al. (2014). In that way, the tests check each rule and overall workflow.

Go to the workflow repository

cd 16S-workflow

Activate Qiime2 environment

conda activate <your env name>

Run the tests

pytest .tests

Reference

Zackular, J. P., Rogers, M. A., Ruffin IV, M. T., & Schloss, P. D. (2014). The human gut microbiome as a screening tool for colorectal cancer. Cancer prevention research, 7(11), 1112-1121.