The test suite

All of the artic tests are run as part of the Travis Continuous Integration testing. To run any of the tests yourself, it is assumed that you have downloaded the codebase and are using an appropiate environment:

git clone
cd fieldbioinformatics
conda env create -f environment.yml
conda activate artic

Unit tests

We have begun writing unit tests for the ARTIC Python modules. These currently includes tests for the align_trim module, which performs amplicon soft clipping and alignment filtering, and vcftagprimersites which processes the ARTIC primer scheme. To run all available unit tests:

pytest -s artic/*

Pipeline tests

To test the core pipeline, you can use the bash script. You can test both the medaka and nanopolish workflows:

./ medaka
./ nanopolish

The pipeline tests use a small subset of an Ebola virus amplicon sequencing run (flongle) which is downloaded from here when the test is called.

Variant validation tests

Finally, we have also included some validation tests that will download several reference SARS-CoV-2 datasets, run the nanopolish/medaka workflows and then validate the reported variants and consensus sequences. To run all of the available validation datasets:

pytest -s artic/

Or you can specify which workflow and how many datasets to validate against:

pytest -s artic/ --workFlow medaka --numValidations 2

use --workFlows to specify workflow (medaka|nanopolish)

use --numValidations to specify how many datasets to download and validate against (specifing -1 or too high a number will just run all the datasets)