Installation

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

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

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

docker run hello-world

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

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

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

pip install nf-core

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

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

export JAVA_HOME=/path/to/java11

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

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