Merge pull request #1 from nservant/master

first push on nf-core dev version

.travis.yml

@@ -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

README.md

-# 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.

nextflow.config

@@ -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