In our daily work we use Nextflow a lot to analyze our huge datasets derived from clinical trials or from our research in Genetics. As part of nf-gwas, we asked ourselves how to test production ready Nextflow pipelines in an efficient and automated way.
When it comes to testing, nf-core already provides a simple python based test-framework that helps comparing output files of a workflow or process with a list of expected files. Nevertheless, an unit-style testing framework is still missing.
We looked across different Groovy based testing frameworks and discovered Spock. It describes itself as a testing and specification framework and was designed for Groovy and Java applications but it gave us an idea what would be possible using the magic of Power Assertions and a kind of behavioral specifications.
So why not just writing simple test scripts with a when and then block using a DSL language that is as similar as possible to Nextflow and a test-runner that executes these scripts?
nf-test was born: a simple and elegant way to describe the expected behaviour of Nextflow pipelines.
nf-test is still a preview version and the syntax and grammar of the DSL could be changed before we release the first stable version. However, we are using nf-test heavily for our in-house pipelines and we think it could be helpful for the community.
A simple example to test the Hello World Nextflow pipeline would look like this:
If you are interested in nf-test and would give it a try, you can read the documentation, try out this tutorial or simple browse the tests we are using in nf-gwas.
