https://github.com/dhslab/nf-core-hicmap

3D genome contacts calling from HiC data

https://github.com/dhslab/nf-core-hicmap

Repository

3D genome contacts calling from HiC data

https://github.com/dhslab/nf-core-hicmap/blob/dev/

# ![dhslab/hicmap](docs/images/nf-core-hicmap_logo_light.png#gh-light-mode-only) ![dhslab/hicmap](docs/images/nf-core-hicmap_logo_dark.png#gh-dark-mode-only)

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## Introduction

**dhslab/hicmap** is a bioinformatics pipeline that ...






1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))

## Usage

> **Note**
> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
> with `-profile test` before running the workflow on actual data.



Now, you can run the pipeline using:



```bash
nextflow run dhslab/hicmap \
   -profile  \
   --input samplesheet.csv \
   --outdir 
```

> **Warning:**
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).

For more details, please refer to the [usage documentation](https://nf-co.re/hicmap/usage) and the [parameter documentation](https://nf-co.re/hicmap/parameters).

## Pipeline output

To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/hicmap/results) tab on the nf-core website pipeline page.
For more details about the output files and reports, please refer to the
[output documentation](https://nf-co.re/hicmap/output).

## Credits

dhslab/hicmap was originally written by Mohamed Mahgoub.

We thank the following people for their extensive assistance in the development of this pipeline:



## 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 the [Slack `#hicmap` channel](https://nfcore.slack.com/channels/hicmap) (you can join with [this invite](https://nf-co.re/join/slack)).

## Citations






An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

You can cite the `nf-core` publication as follows:

> **The nf-core framework for community-curated bioinformatics pipelines.**
>
> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
>
> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).

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