Chapter 2 Dependencies

The pipeline runs on nextflow a domain-specific language created to automate data-analysis pipelines whilst maximising reproducibility. Nextflow enables scientists to focus on their analyses, isolating different parts of the pipeline into processes whose dependencies can be dealt with using containers and virtual environments with technologies such as Docker, Singularity, and Anaconda.

The recommended way to install nextflow is via conda, using the environment file.

conda env create -f nextflow_conda_env.yml # will create an env called "nextflow"
conda activate nextflow
# You can edit the file at your choice, specially if the environment name conflicts
# with a preexisting conda env on your system

Docker should be installed as well:

sudo apt install docker

Once nextflow is installed, it will automatically retrieve the docker images used within the pipeline.