anthropics--knowledge-work-plugins/bio-research/skills/nextflow-development/references/installation.md

Installation

Contents

• Quick install
• Docker setup
• Singularity setup (HPC)
• nf-core tools (optional)
• Verify installation
• Common issues

Quick install

# Nextflow
curl -s https://get.nextflow.io | bash
mv nextflow ~/bin/
export PATH="$HOME/bin:$PATH"

# Verify
nextflow -version
java -version  # Requires 11+

Docker setup

Linux

sudo apt-get update && sudo apt-get install docker.io
sudo systemctl enable --now docker
sudo usermod -aG docker $USER
# Log out and back in

macOS

Download Docker Desktop: https://docker.com/products/docker-desktop

Verify

docker run hello-world

Singularity setup (HPC)

# Ubuntu/Debian
sudo apt-get install singularity-container

# Or via conda
conda install -c conda-forge singularity

Configure cache

export NXF_SINGULARITY_CACHEDIR="$HOME/.singularity/cache"
mkdir -p $NXF_SINGULARITY_CACHEDIR
echo 'export NXF_SINGULARITY_CACHEDIR="$HOME/.singularity/cache"' >> ~/.bashrc

nf-core tools (optional)

pip install nf-core

Useful commands:

nf-core list                    # Available pipelines
nf-core launch rnaseq           # Interactive parameter selection
nf-core download rnaseq -r 3.14.0  # Download for offline use

Verify installation

nextflow run nf-core/demo -profile test,docker --outdir test_demo
ls test_demo/

Common issues

Java version wrong:

export JAVA_HOME=/path/to/java11

Docker permission denied:

sudo usermod -aG docker $USER
# Log out and back in

Nextflow not found:

echo 'export PATH="$HOME/bin:$PATH"' >> ~/.bashrc
source ~/.bashrc