#  
[](https://nf-co.re/hic/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)
[](https://www.nextflow.io/)
[](https://docs.conda.io/en/latest/)
[](https://www.docker.com/)
[](https://sylabs.io/docs/)
[](https://tower.nf/launch?pipeline=https://github.com/nf-core/hic)
[](https://nfcore.slack.com/channels/hic)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)
## Introduction
**nf-core/hic** is a bioinformatics pipeline that ...
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Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
major pipeline sections and the types of output it produces. You're giving an overview to someone new
to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
-->
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workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. -->
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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.
<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
Explain what rows and columns represent. For instance (please edit as appropriate):
First, prepare a samplesheet with your input data that looks as follows:
`samplesheet.csv`:
```csv
sample,fastq_1,fastq_2
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
```
Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
-->
Now, you can run the pipeline using:
<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
```bash
nextflow run nf-core/hic \
-profile <docker/singularity/.../institute> \
--input samplesheet.csv \
--outdir <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/hic/usage) and the [parameter documentation](https://nf-co.re/hic/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/hic/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/hic/output).
## Credits
nf-core/hic was originally written by Nicolas Servant.
We thank the following people for their extensive assistance in the development of this pipeline:
<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
## 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 `#hic` channel](https://nfcore.slack.com/channels/hic) (you can join with [this invite](https://nf-co.re/join/slack)).
## Citations
<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
<!-- If you use nf-core/hic for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
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).