tools

<h1> <picture> <source media="(prefers-color-scheme: dark)" srcset="docs/images/nfcore-tools_logo_dark.png"> <img alt="nf-core/tools" src="docs/images/nfcore-tools_logo_light.png"> </picture> </h1><!-- omit in toc -->

A python package with helper tools for the nf-core community.

Read this documentation on the nf-core website: https://nf-co.re/tools

Table of contents <!-- omit in toc -->

• nf-core tools installation

• nf-core tools update

• nf-core list - List available pipelines

• nf-core launch - Run a pipeline with interactive parameter prompts

• nf-core create-params-file - Create a parameter file

• nf-core download - Download a pipeline for offline use

• nf-core licences - List software licences in a pipeline

• nf-core create - Create a new pipeline with the nf-core template

• nf-core lint - Check pipeline code against nf-core guidelines

• nf-core schema - Work with pipeline schema files

• nf-core bump-version - Update nf-core pipeline version number

• nf-core sync - Synchronise pipeline TEMPLATE branches

• nf-core create-logo - Create an nf-core pipeline logo

• nf-core tui - Explore the nf-core command line graphically

• nf-core modules - commands for dealing with DSL2 modules

  • modules list - List available modules
    • modules list remote - List remote modules
    • modules list local - List installed modules
  • modules info - Show information about a module
  • modules install - Install modules in a pipeline
  • modules update - Update modules in a pipeline
  • modules remove - Remove a module from a pipeline
  • modules patch - Create a patch file for a module
  • modules create - Create a module from the template
  • modules lint - Check a module against nf-core guidelines
  • modules test - Run the tests for a module
  • modules bump-versions - Bump software versions of modules

• nf-core subworkflows - commands for dealing with subworkflows

  • subworkflows list - List available subworkflows
    • subworkflows list remote - List remote subworkflows
    • subworkflows list local - List installed subworkflows
  • subworkflows info - Show information about a subworkflow
  • subworkflows install - Install subworkflows in a pipeline
  • subworkflows update - Update subworkflows in a pipeline
  • subworkflows remove - Remove a subworkflow from a pipeline
  • subworkflows create - Create a subworkflow from the template
  • subworkflows lint - Check a subworkflow against nf-core guidelines
  • subworkflows test - Run the tests for a subworkflow

• Citation

The nf-core tools package is written in Python and can be imported and used within other packages. For documentation of the internal Python functions, please refer to the Tools Python API docs.

Installation

Bioconda

You can install nf-core/tools from bioconda.

First, install conda and configure the channels to use bioconda (see the bioconda documentation). Then, just run the conda installation command:

conda install nf-core

Alternatively, you can create a new environment with both nf-core/tools and nextflow:

conda create --name nf-core python=3.12 nf-core nextflow
conda activate nf-core

Python Package Index

nf-core/tools can also be installed from PyPI using pip as follows:

pip install nf-core

Docker image

There is a docker image that you can use to run nf-core/tools that has all of the requirements packaged (including Nextflow) and so should work out of the box. It is called nfcore/tools (NB: no hyphen!)

You can use this container on the command line as follows:

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

• -i and -t are needed for the interactive cli prompts to work (this tells Docker to use a pseudo-tty with stdin attached)
• The -v argument tells Docker to bind your current working directory (pwd) to the same path inside the container, so that files created there will be saved to your local file system outside of the container.
• -w sets the working directory in the container to this path, so that it's the same as your working directory outside of the container.
• -u sets your local user account as the user inside the container, so that any files created have the correct ownership permissions

After the above base command, you can use the regular command line flags that you would use with other types of installation. For example, to launch the viralrecon pipeline:

docker run -itv `pwd`:`pwd` -w `pwd` -u $(id -u):$(id -g) nfcore/tools launch viralrecon -r 1.1.0

If you use $NXF_SINGULARITY_CACHEDIR for downloads, you'll also need to make this folder and environment variable available to the continer:

docker run -itv `pwd`:`pwd` -w `pwd` -u $(id -u):$(id -g) -v $NXF_SINGULARITY_CACHEDIR:$NXF_SINGULARITY_CACHEDIR -e NXF_SINGULARITY_CACHEDIR nfcore/tools launch viralrecon -r 1.1.0

Docker bash alias

The above base command is a bit of a mouthful to type, to say the least. To make it easier to use, we