What is Nextflow and How to Use it?

Renesh Bedre    1 minute read

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 curl and conda.

Nextflow requires Java 11 or later for installation. For instructions on how to install Java, click here.

Install Nextflow using curl

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 nextflow file for directly executing the nextflow command.

Install Nextflow using conda

conda install nextflow

How to launch Nextflow pipeline?

You can launch the nextflow pipeline using the run command:

./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.

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