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Unverified Commit 02ba7d26 authored by Nicolas Servant's avatar Nicolas Servant Committed by GitHub
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Merge pull request #1 from nservant/master

first push on nf-core dev version
parents a8ea256a c2e3fbab
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......@@ -11,9 +11,9 @@ before_install:
# PRs to master are only ok if coming from dev branch
- '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
# Pull the docker image first so the test doesn't wait for this
- docker pull nservant/nf-core-hic:dev
- docker pull nfcore/hic:dev
# Fake the tag locally so that the pipeline runs properly
- docker tag nservant/nf-core-hic:dev nservant/nf-core-hic:latest
- docker tag nfcore/hic:dev nfcore/hic:latest
install:
# Install Nextflow
......
# nf-core/hic
# ![nf-core/hic](docs/images/nfcore-rnaseq_logo.png)
**Analysis of Chromosome Conformation Capture data (Hi-C)**
[![Build Status](https://travis-ci.org/nf-core/hic.svg?branch=master)](https://travis-ci.org/nf-core/hic)
......@@ -10,8 +11,20 @@
https://img.shields.io/badge/singularity-available-7E4C74.svg)
### Introduction
This pipeline is based on the [HiC-Pro workflow](https://github.com/nservant/HiC-Pro).
It was designed to process Hi-C data from raw fastq files (paired-end Illumina data) to normalized contact maps. The current version supports digestion protocols.
Support for other protocols is ongoing.
The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.
### Pipeline summary
1. Mapping using a two steps strategy to rescue reads spanning the ligation sites (bowtie2)
2. Detection of valid interaction products
3. Duplicates removal
4. Create genome-wide contact maps at various resolution
5. Contact maps normalization using the ICE algorithm (iced)
6. Quality controls and report (MultiQC)
7. Addition export for visualisation and downstream analysis (cooler)
### Documentation
The nf-core/hic pipeline comes with documentation about the pipeline, found in the `docs/` directory:
......@@ -25,7 +38,5 @@ The nf-core/hic pipeline comes with documentation about the pipeline, found in t
4. [Output and how to interpret the results](docs/output.md)
5. [Troubleshooting](docs/troubleshooting.md)
<!-- TODO nf-core: Add a brief overview of what the pipeline does and how it works -->
### Credits
nf-core/hic was originally written by Nicolas Servant.
......@@ -14,7 +14,7 @@ params {
// Container slug. Stable releases should specify release tag!
// Developmental code should specify :latest
//container = 'nfcore/hic:latest'
container = 'nservant/nf-core-hic:latest'
container = 'nfcore/hic:latest'
// Workflow flags
// TODO nf-core: Specify your pipeline's command line flags
......
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