Installing Nextflow

Nextflow is the workflow management system that runs all nf-core pipelines. This page will walk you through installing and configuring Nextflow on your system.

Install Java

The easiest way to install Java is using SDKMAN:

1. Install SDKMAN:

   curl -s https://get.sdkman.io | bash

2. Open a new terminal.

3. Install Java:

   sdk install java 17.0.10-tem

4. Confirm that Java is installed correctly:

   java -version

Install Nextflow

Nextflow is distributed as an easy to use self-installing package. It is also distributed via Conda and as a standalone distribution.

The self-installing package is recommended as it ensures you always get the latest version and handles dependencies automatically.

Self-installing package

To install Nextflow with the self-installing package:

1. Download and install Nextflow:

   curl -s https://get.nextflow.io | bash

2. Make the binary executable:

   chmod +x nextflow

3. Move Nextflow to a directory in your $PATH:

   mkdir -p $HOME/.local/bin/
   mv nextflow $HOME/.local/bin/

   Note

   Common directories on Linux or OSX operating systems for executables include $HOME/.local/bin/, /usr/local/bin/, or $HOME/bin/. Make sure the directory you choose is in your $PATH environment variable.

4. Verify the installation:

   nextflow info

Conda installation

To install Nextflow with Conda:

1. Create an environment with Nextflow:

   conda create --name nf-env bioconda::nextflow

2. Activate the environment:

   source activate nf-env

3. Confirm Nextflow is installed correctly:

   nextflow infoactivate nf-env

Standalone distribution

For offline or restricted environments, you can download a pre-built executable from the Nextflow GitHub releases.

To use the standalone distribution:

1. Download the standalone distribution from Assets section of the GitHub releases page.

2. Grant execution permissions to the downloaded file. For example:

   chmod +x nextflow-25.10.0-dist

3. Use it as a drop-in replacement for nextflow command. For example:

   ./nextflow-25.10.0-dist run info

Replace 25.10.0 with your desired version number.

Update Nextflow

To use the latest Nextflow features or run specific versions of pipelines, you may need to update or pin your version of Nextflow.

Update to the latest stable version

To update Nextflow to the latest stable release, run:

nextflow self-update

Pin a specific version

To pin a specific Nextflow version:

• For a single command, prefix the Nextflow command with the NXF_VER variable:

  NXF_VER=23.10.0 nextflow run nf-core/rnaseq

• For your current terminal session, export the NXF_VER variable:

  export NXF_VER=23.10.0

• For persistent usage, add the export NXF_VER variable command to ~/.bashrc or ~/.zshrc:

  export NXF_VER=23.10.0