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Commit f54bf1e1 authored by nservant's avatar nservant
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update README

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......@@ -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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