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.