What is Nextflow and How to Use it?
What is Nextflow?
Nextflow is a workflow language for creating scalable, shareable, and reproducible computational pipelines for automating multiple tasks in a single workflow.
Nextflow is a domain-specific language (DSL) and simplifies computational pipeline development for complex bioinformatics data analysis.
Nextflow allows workflows to be separated from execution environments. As a result, you can run the same computation pipeline on your local machine, a cluster of HPC machines, or in the cloud.
Nextflow is language independent and supports any programming language (for example, Python, Bash, Perl, Ruby, etc.). In addition, Nextflow supports Docker, Singularity, conda, and AWS technologies.
The nextflow has more features, has greater community support, and is widely used to develop bioinformatics pipelines compared to Snakemake.
How to install Nextflow?
Nextflow can be installed easily using
Nextflow requires Java 11 or later for installation. For instructions on how to install Java, click here.
Install Nextflow using
curl -s https://get.nextflow.io | bash
Once you execute the above command successfully, you should see a
nextflow executable file in the current directory.
Tip: You can also add the PATH to the executable
nextflowfile for directly executing the
Install Nextflow using
conda install nextflow
How to launch Nextflow pipeline?
You can launch the
nextflow pipeline using the
./nextflow run hello
You should see the following output after executing the above command
N E X T F L O W ~ version 23.04.1 Pulling nextflow-io/hello ... downloaded from https://github.com/nextflow-io/hello.git Launching `https://github.com/nextflow-io/hello` [cheeky_avogadro] DSL2 - revision: 1d71f857bb [master] executor > local (4) [51/ad8061] process > sayHello (4) [100%] 4 of 4 ✔ Bonjour world! Ciao world! Hello world! Hola world!
Similarly, you can run the Nextflow pipelines (with
.nf extension) using the
nextflow run command.
Enhance your skills with courses on genomics and bioinformatics
- Genomic Data Science Specialization
- Biology Meets Programming: Bioinformatics for Beginners
- Python for Genomic Data Science
- Bioinformatics Specialization
- Command Line Tools for Genomic Data Science
This work is licensed under a Creative Commons Attribution 4.0 International License
Some of the links on this page may be affiliate links, which means we may get an affiliate commission on a valid purchase. The retailer will pay the commission at no additional cost to you.