README.md

nextflow pipeline

This repository is a template and a library repository to help you build nextflow pipeline. You can fork this repository to build your own pipeline. To get the last commits from this repository into your fork use the following commands:

git remote add upstream https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow.git
git pull upstream master

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

To run nextflow on you computer you need to have java (>= 1.8) installed.

java --version

To be able to easily test tools already implemented for nextflow on your computer (src/nf_modules/ to see their list). You need to have docker installed.

docker run hello-world

Installing

To install nextflow on you computer simply run the following command:

src/install_nextflow.sh

Then to initialise a given tools run the following command:

src/docker_modules/<tool_name>/<tool_version>/docker_init.sh

for example to initialise file_handle version 0.1.1, run:

src/docker_modules/file_handle/0.1.1/docker_init.sh

To initialise all the tools:

find src/docker_modules/ -name "docker_init.sh" | awk '{system($0)}'

Running the tests