nf-test: A simple testing framework
for Nextflow pipelines

Test your production ready Nextflow pipelines in an efficient and automated way. 🚀

A DSL language similar to Nextflow
Describes expected behavior using 'when' and 'then' blocks
Abundance of functions for writing elegant and readable assertions
Utilizes snapshots to write tests for complex data structures
Provides commands for generating boilerplate code
Includes a test-runner that executes these scripts
Easy installation on CI systems

Unit testing

nf-test enables you to test all components of your data science pipeline: from end-to-end testing of the entire pipeline to specific tests of processes or even custom functions. This ensures that all testing is conducted consistently across your project.

Pipeline Process Functions

nextflow_pipeline {

  name "Test Hello World"
  script "nextflow-io/hello"

  test("hello world example should start 4 processes") {
    expect {
      with(workflow) {
        assert success
        assert trace.tasks().size() == 4
        assert "Ciao world!" in stdout
        assert "Bonjour world!" in stdout
        assert "Hello world!" in stdout
        assert "Hola world!" in stdout
      }
    }
  }

}

nextflow_process {

    name "Test Process SALMON_INDEX"
    script "modules/local/salmon_index.nf"
    process "SALMON_INDEX"

    test("Should create channel index files") {

        when {
            process {
                """
                input[0] = file("test_data/transcriptome.fa")
                """
            }
        }

        then {
            //check if test case succeeded
            assert process.success
            //analyze trace file
            assert process.trace.tasks().size() == 1
            with(process.out) {
                // check if emitted output has been created
                assert index.size() == 1
                // count amount of created files
                assert path(index.get(0)).list().size() == 16
                // parse info.json file
                def info = path(index.get(0)+'/info.json').json
                assert info.num_kmers == 375730
                assert info.seq_length == 443050
                //verify md5 checksum
                assert path(index.get(0)+'/info.json').md5 == "80831602e2ac825e3e63ba9df5d23505"
            }
        }

    }

}

nextflow_function {

    name "Test functions"
    script "functions.nf"

    test("Test function1") {
      function "function1"
      ...
    }

    test("Test function2") {
      function "function2"
      ...
    }
}

Learn more about pipeline tests, workflow tests, process tests and function tests in the documentation.

Snapshot testing

nf-test supports snapshot testing and automatically generates a baseline set of unit tests to safeguard against regressions caused by changes.
nf-test captures a snapshot of output channels or any other objects and subsequently compares them to reference snapshot files stored alongside the tests. If the two snapshots do not match, the test will fail

Learn more

Highly extendable

nf-test supports the inclusion of third-party libraries (e.g., jar files) or functions from Groovy files. This can be done to either extend its functionality or to prevent code duplication, thus maintaining simplicity in the logic of test cases. Given that many assertions are specific to use cases, nf-test incorporates a plugin system that allows for the extension of existing classes with custom methods. For example FASTA file support.

Learn more

Support us

We love stars as much as we love rockets! So make sure you star us on GitHub.

Star

Show the world your Nextflow pipeline is using nf-test and add the following badge to your README.md:

[![nf-test](https://img.shields.io/badge/tested_with-nf--test-337ab7.svg)](https://code.askimed.com/nf-test)

Citation

If you test your pipeline with nf-test, please cite:

Forer, L., & Schönherr, S. (2024). Improving the Reliability and Quality of Nextflow Pipelines with nf-test. bioRxiv. https://doi.org/10.1101/2024.05.25.595877

About

nf-test has been created by Lukas Forer and Sebastian Schönherr and is MIT Licensed.

Thanks to all the contributors to help us maintaining and improving nf-test!

nf-test: A simple testing framework for Nextflow pipelines