Sarek pipeline orchestration for the GOAL Consortium

This repository contains documentation and scripts to help clinical labs deploy the nf-core Sarek pipeline.

Quick Start

If you don't have nextflow and singularity, see section below. If you do, use them to test Sarek on its included test data:

nextflow run -bg -profile test,singularity -work-dir nf_work -revision 2.7.1 nf-core/sarek --tools Mutect2 --outdir test_results

Install Nextflow and Singularity

mamba is a fast alternative to conda, a package manager that can download and install specific versions of software in isolated environments, very useful in data-science projects. mambaforge is a variant of miniforge that installs mamba configured with conda-forge as the default source of packaged software.

These instructions show you how to install mamba, and then use it to install nextflow and singularity for executing popular bioinformatics pipelines. Unfortunately, singularity is not available on Windows or macOS. So, this guide will only target Linux environments. If you have to use Windows 10, then try WSL2. If you have to use macOS, then try a Virtual Machine.

Download the mambaforge installer for Linux environments:

curl -L https://github.com/conda-forge/miniforge/releases/download/4.10.3-7/Mambaforge-Linux-x86_64.sh -o mambaforge.sh

Install mamba into a folder named mambaforge under your home directory, and delete the installer:

sh mambaforge.sh -bfp $HOME/mambaforge && rm -f mambaforge.sh

Add the following to your ~/.bashrc file to activate the base environment whenever you login:

# Add mambaforge to PATH if found, and load the base environment
if [ -f "$HOME/mambaforge/etc/profile.d/conda.sh" ]; then
    . $HOME/mambaforge/etc/profile.d/conda.sh
    conda activate
fi

Logout and login to activate the base environment, install necessary packages, and cleanup cached packages:

mamba install -y -c bioconda git==2.33.1 openjdk==11.0.8 nextflow==21.10.0 singularity==3.8.4
mamba clean -ay