README.md

# Meta HiC pipeline: Documentation

The Meta HiC pipeline is split into the following pages:

- [Usage hicpro workflow](usage.md)
  - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags for the hicpro workflow.
- [Usage hicstuff workflow](hicstuff_usage.md)
  - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags for the hicstuff workflow.
- [Output](output.md)
  - /!\TO UPDATE/!\ An overview of the different results produced by the pipeline and how to interpret them.

You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re)