Quantitative nucleosome and Chip-Seq pipeline

This repository contains 3 differents pipelines:

• A chip_analysis.nf for classical Chip-Seq analysis: README_chip.md
• A mnase_mapping.nf and mnase_analysis.nf for nucleosome data analysis: README_chip.md
• A chip_quant_analysis.nf for quantitative Chip-Seq analysis: README_chip.md

Getting the last updates

To get the last commits from this repository into your fork use the following commands:

For the first time:

git remote add upstream git@gitbio.ens-lyon.fr:LBMC/nextflow.git
git pull upstream master

Then to make an update:

git pull upstream master
git merge upstream/master

Getting Started

These instructions will get you a copy of the project as a template when you want to build your own pipeline.

you can follow them here.

Building your pipeline

You can follow the building your pipeline guide for a gentle introduction to nextflow and taking advantage of this template to build your pipelines.

Existing Nextflow pipeline

Before starting a new project, you can check if someone else didn’t already to the work !

• on the nextflow project page
• on the nf-core project

Contributing

If you want to add more tools to this project, please read the CONTRIBUTING.md.

Authors

• Laurent Modolo - Initial work

See also the list of contributors who participated in this project.

License

This project is licensed under the CeCiLL License- see the LICENSE file for details