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 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 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.

Install Java

The easiest way to install it is using SDKMAN:

To install Java with 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

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

Update to the latest edge version

To update to the latest edge release, run:

NXF_EDGE=1 nextflow self-update

To update to the latest stable release, run:

NXF_EDGE=0 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

Troubleshooting

Java version issues

Problem: Error about incompatible Java version

Solution: Ensure you have Java 17 or later installed. Check your version with java -version and install a compatible version using SDKMAN (see Install Java).

Permission denied errors

Problem: Cannot execute Nextflow after installation

Solution: Make sure the Nextflow executable has execution permissions:

chmod +x /path/to/nextflow

Update failures

Problem: nextflow self-update fails

Solution: The update can fail if Nextflow is installed in a directory with restricted permissions. Either:

• Request elevated permissions to update in the current location
• Reinstall Nextflow in a directory where you have write permissions

Command not found

Problem: nextflow: command not found

Solution: Ensure Nextflow is in a directory included in your $PATH. Add the directory to your PATH by adding this line to ~/.bashrc or ~/.zshrc:

export PATH="$HOME/.local/bin:$PATH"

Then reload your shell configuration:

source ~/.bashrc  # or source ~/.zshrc

Conda installation issues

Problem: Outdated Nextflow version or dependency conflicts with Conda

Solution: Uninstall the Conda version and use the self-installing package method instead:

conda deactivate
conda remove --name nf-env --all
curl -s https://get.nextflow.io | bash

Checking for migration requirements

Problem: Pipeline fails after updating Nextflow

Solution: When updating across major stable releases, consult the Nextflow migration guides and changelog for breaking changes that may affect your pipelines.

Additional resources

For more information about installing Nextflow, see:

• Nextflow installation