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 in a dedicated environment with 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
Note

When using pip, ensure you have Python 3.8 or later installed. You may need to use pip3 instead of pip depending on your system configuration.

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:

  1. Activate the environment:

    conda activate nf-core-env

  2. Run the update command:

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
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