https://github.com/askimed/nf-test
Simple test framework for Nextflow pipelines
https://github.com/askimed/nf-test
nextflow test-automation testing testing-tools
Last synced: 5 months ago
JSON representation
Simple test framework for Nextflow pipelines
- Host: GitHub
- URL: https://github.com/askimed/nf-test
- Owner: askimed
- License: mit
- Created: 2021-10-18T14:18:07.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2025-11-03T06:14:08.000Z (8 months ago)
- Last Synced: 2026-01-11T23:53:08.061Z (5 months ago)
- Topics: nextflow, test-automation, testing, testing-tools
- Language: Java
- Homepage: https://www.nf-test.com
- Size: 5.91 MB
- Stars: 174
- Watchers: 8
- Forks: 36
- Open Issues: 113
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# :rocket: nf-test
> Simple test framework for Nextflow pipelines
The full documentation can be found [here](https://code.askimed.com/nf-test).
## 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:
```bash
curl -fsSL https://get.nf-test.com | bash
```
If you don't have curl installed, you could use wget:
```bash
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](https://code.askimed.com/nf-test).
## Badge
Show the world your Nextflow pipeline is using nf-test:
[](https://github.com/askimed/nf-test)
```
[](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](https://doi.org/10.1101/2024.05.25.595877)
## Contact
- Lukas Forer [@lukfor](https://twitter.com/lukfor)
- Sebastian Schönherr [@seppinho](https://twitter.com/seppinho)