From f54bf1e1245720707c339dea222ec3b9254d6b23 Mon Sep 17 00:00:00 2001
From: nservant <nservant@curie.fr>
Date: Mon, 14 Oct 2019 17:23:21 +0200
Subject: [PATCH] update README

---
 README.md | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/README.md b/README.md
index e59b529..cbe9ba2 100644
--- a/README.md
+++ b/README.md
@@ -39,6 +39,28 @@ sites (bowtie2)
 6. Quality controls and report (MultiQC)
 7. Addition export for visualisation and downstream analysis (cooler)
 
+## Quick Start
+
+i. Install [`nextflow`](https://nf-co.re/usage/installation)
+
+ii. Install one of [`docker`](https://docs.docker.com/engine/installation/),
+[`singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or
+[`conda`](https://conda.io/miniconda.html)
+
+iii. Download the pipeline and test it on a minimal dataset with a single command
+
+```bash
+nextflow run hic -profile test,<docker/singularity/conda>
+```
+
+iv. Start running your own analysis!
+
+```bash
+nextflow run hic -profile <docker/singularity/conda> --reads '*_R{1,2}.fastq.gz' --genome GRCh37
+```
+
+See [usage docs](docs/usage.md) for all of the available options when running the pipeline.
+
 ## Documentation
 
 The nf-core/hic pipeline comes with documentation about the pipeline, found in
@@ -53,6 +75,16 @@ the `docs/` directory:
 4. [Output and how to interpret the results](docs/output.md)
 5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
 
+## Contributions and Support
+
+If you would like to contribute to this pipeline, please see the
+[contributing guidelines](.github/CONTRIBUTING.md).
+
+For further information or help, don't hesitate to get in touch on
+[Slack](https://nfcore.slack.com/channels/hic).
+You can join with [this invite](https://nf-co.re/join/slack).
+
+
 ## Credits
 
 nf-core/hic was originally written by Nicolas Servant.
-- 
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