A Nextflow pipeline for Common Phage Immuno-Precipitation Sequencing experiments. See the Documentation for more details and usage examples.

Install Nextflow by using the following command:

curl -s https://get.nextflow.io | bash 

Download the Docker Desktop, there exists several distributions packaged for various linux flavors

curl -fsSL https://get.docker.com -o get-docker.sh && sudo sh get-docker.sh

Launch the pipeline execution with the following command:

nextflow run matsengrp/phip-flow -r V1.12 -profile docker

Note: the -r VX.XX command runs the specified stable release version of the pipeline. For running the bleeding edge (not generally recommended) you may also specify -r main. You may also specify any of the parameters for changing the input data and workflow behavior.

Note: the phippery Dockerfile contains all the required dependencies except those for EdgeR and BEER, for which the maintainers of that package host their own public image.