Environment setup

To work with nf-core pipelines, you will need to set up your computing environment with some essential tools. This section guides you through installing and configuring everything you need to get started.

What you’ll need

The core requirements for running nf-core pipelines are:

1. Nextflow: The workflow management system that powers all nf-core pipelines
2. Container or compute environment manager: A system to handle pipeline software (e.g., Docker, Singularity, or Conda)

These additional tools are recommended for development:

1. nf-core tools: Command-line tools for working with nf-core pipelines (optional, but recommended)
2. VS Code: A code editor with an official Nextflow extension (optional, for pipeline development)
3. Prettier: A code styling autoformatter used in multiple nf-core repositories (optional, but recommended)

Getting started

If you are new to running nf-core pipelines, we recommend the following guides:

1. Install Nextflow
2. Set up a Container or compute environment manager based on your system

If you are new to developing pipelines, we recommend the following additional guides:

1. Install nf-core tools for additional utilities and pipeline management features
2. Set up VS Code with the recommended extensions if you plan to develop pipelines
3. Set up Prettier with pre-commit so you can have auto-formatting of your code before pushing to GitHub

Need help?

If you encounter issues during setup, check our troubleshooting guide for solutions to common problems with Nextflow, nf-core tools, and development environments.

Still stuck? The nf-core community is here to help! Join us on Slack where you can ask questions, get support, and connect with other users and developers.