:rocket: nf-test

Simple test framework for Nextflow pipelines The full documentation can be found here.

Installation

nf-test has the same requirements as Nextflow and can be used on POSIX compatible systems like Linux or OS X. You can install nf-test using the following command:

curl -fsSL https://get.nf-test.com | bash

If you don't have curl installed, you could use wget:

wget -qO- https://get.nf-test.com | bash

It will create the nf-test executable file in the current directory. Optionally, move the nf-test file to a directory accessible by your $PATH variable.

Conda

To install this package from Bioconda run the following command:

conda install -c bioconda nf-test

Note: this recipe is not maintained by us.

Compile from source

To compile nf-test from source you shall have maven installed. This will produce a nf-test/target/nf-test.jar file.

git clone git@github.com:askimed/nf-test.git
cd nf-test
mvn install

To use the newly compiled nf-test.jar, update the nf-test bash script that is on your PATH to point to the new .jar file. First locate it with which nf-test, and then modify APP_HOME and APP_JAR vars at the top:

#!/bin/bash
APP_HOME="/PATH/TO/nf-test/target/"
APP_JAR="nf-test.jar"
APP_UPDATE_URL="https://code.askimed.com/install/nf-test"
...

Usage

nf-test test example/*.nf.test

The full documentation can be found here.

Badge

Show the world your Nextflow pipeline is using nf-test:

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

Contact

• Lukas Forer @lukfor
• Sebastian Schönherr @seppinho