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connor-lab / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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Add github ci test workflow, scripts and data. #35

Closed sb10 closed 4 years ago

sb10 commented 4 years ago

These tests make use of free github CI features to run tests on PRs that want to merge to master.

To make use of them therefore, you should prepare all code changes in branches, push the branch, and then create a PR of it against master. Wait for the tests to run, and merge when they pass.

Currently the tests take ~25mins+ to run because they have to build the singularity image. The tests can be altered in the future as appropriate when the singularity image is in a hub, and then the tests will only take a few mins to run.

If a test fails, the reason for the failure can be found by downloading the test artifacts and looking at the test_artifact.log and nextflow.log files.

These tests only cover the illumina mode. They would have caught a number of workflow-breaking commits that have made it to master in our own fork and in this repo, so we believe them to be very valuable. It should be possible to copy the scripts to develop tests for the other modes as well, to also make sure those don't get accidentally broken.

One of the tests compares current code against a certain past commit. It is intended that once v1 is tagged, the test is changed so that future PRs are tested against v1.

m-bull commented 4 years ago

Thanks Sendu and WSI team - this is incredibly helpful.