nf-core tools

nf-core tools is a Python package that provides command-line utilities for working with nf-core pipelines. While optional, it offers helpful features for downloading, launching, and developing pipelines.

The nf-core tools package provides commands for:

• Listing available nf-core pipelines and components
• Downloading pipelines for offline use
• Launching pipelines with customized parameters
• Creating and developing new pipelines and components
• Linting and validating pipeline code

Installing nf-core tools

nf-core tools can be installed using Conda, pip, or Docker. Choose the method that best fits your environment.

Install with Conda

Conda is the recommended installation method as it handles all dependencies automatically.

To install nf-core tools with Conda:

1. Install nf-core tools in your current environment:

   conda install nf-core

2. Verify the installation:

   nf-core --version

Alternatively, create a dedicated environment with both nf-core tools and Nextflow:

1. Create a new environment:

   conda create --name nf-core-env nf-core nextflow

2. Activate the environment:

   conda activate nf-core-env

3. Verify the installation:

   nf-core --version
   nextflow -version

Install with pip

To install nf-core tools with pip:

1. Install the package:

   pip install nf-core

2. Verify the installation:

   nf-core --version

Install with Docker

To use nf-core tools with Docker:

1. Pull the nfcore/tools Docker image:

   docker pull nfcore/tools

2. Run nf-core tools commands using Docker:

   docker run -itv `pwd`:`pwd` -w `pwd` -u $(id -u):$(id -g) nfcore/tools --help

3. (Optional) Create an alias to simplify commands:

   1. Add an alias in your ~/.bashrc or ~/.zshrc

      alias nf-core="docker run -itv \`pwd\`:\`pwd\` -w \`pwd\` -u $(id -u):$(id -g) nfcore/tools"

   2. Run nf-core directly:

      nf-core --help

Updating nf-core tools

To keep nf-core tools up to date with the latest features and bug fixes, update regularly using your installation method.

Update Conda install

To update your nf-core tools Conda install, run:

conda update nf-core

Update pip install

To update your nf-core tools pip install, run:

pip install --upgrade nf-core

Update Docker install

To update nf-core tools docker image, run:

docker pull nfcore/tools

Troubleshooting

Command not found

Problem: nf-core: command not found

Solution: Ensure nf-core tools is installed in an active environment:

• For Conda: Run conda activate nf-core-env if you installed in a separate environment
• For pip: Ensure the Python scripts directory is in your $PATH
• For Docker: Check that your alias is properly configured in your shell

Python version issues

Problem: Installation fails due to Python version

Solution: nf-core tools requires Python 3.8 or later. Check your version with:

python --version

If necessary, install a newer Python version using Conda:

conda create --name nf-core-env python=3.11 nf-core

Permission errors with pip

Problem: Permission denied when installing with pip

Solution: Install in your user directory instead:

pip install --user nf-core

Or use a virtual environment:

python -m venv nf-core-venv
source nf-core-venv/bin/activate
pip install nf-core

Docker file permissions

Problem: Files created by Docker have wrong ownership

Solution: Always include the -u $(id -u):$(id -g) flag when running Docker commands, or use the alias provided in the Docker installation section.

Additional resources

For more information about installing nf-core tools, see:

• nf-core tools install