nf-core-user-docs

Install Nextflow and nf-core within a Conda Environment

This guide describes the process of configuring conda and creating a conda environment with Nextflow and nf-core installed.

These instructions require that you have the miniconda distribution of conda available as a personal software module. Please refer to the relevant section of Running Nextflow with nf-core Pipelines on TUoS Stanage Cluster if you have not already setup miniconda as a personal software module.

Load and Configure Conda

Run the following commands in the order provided and follow any prompts as appropriate:

# load the miniconda module
module load miniconda

# disable base environment auto-activation
conda config --set auto_activate_base false

# add the bioconda and conda-forge channels to conda configuration
conda config --add channels bioconda
conda config --add channels conda-forge

# set channel_priority to "strict"
conda config --set channel_priority strict

# ensure conda is up-to-date
conda update conda

Create a Conda Analysis Environment with Nextflow and nf-core

Run the following commands in order and follow any prompts as appropriate:

# make the "nf_env" environment
conda create --name nf_env nextflow nf-core

# activate the environment
source activate nf_env

# ensure all packages are up-to-date
conda update --all

You can now test the install has worked by running the following:

# test the environment is working
nextflow info

# test functionality
nextflow run hello

When you are finished, you can deactivate your conda environment using the command conda deactivate

Should you wish to unload your personal miniconda module you can do so by running module unload miniconda

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