diff --git a/README.md b/README.md index e59b529e1547005ba26c369561b8aba9009a9316..cbe9ba2ca552fb8eb230d73600460b013484f719 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.