Prettier changes

[CUT&RUN](https://elifesciences.org/articles/46314)

> Meers, M. P., Bryson, T. D., Henikoff, J. G., & Henikoff, S. (2019). Improved CUT&RUN chromatin profiling tools. *eLife*, *8*. https://doi.org/10.7554/eLife.46314

> Meers, M. P., Bryson, T. D., Henikoff, J. G., & Henikoff, S. (2019). Improved CUT&RUN chromatin profiling tools. _eLife_, _8_. https://doi.org/10.7554/eLife.46314

[CUT&Tag](https://www.nature.com/articles/s41467-019-09982-5)

> Kaya-Okur, H. S., Wu, S. J., Codomo, C. A., Pledger, E. S., Bryson, T. D., Henikoff, J. G., Ahmad, K., & Henikoff, S. (2019). CUT&Tag for efficient epigenomic profiling of small samples and single cells. *Nature Communications*, *10*(1), 1930. https://doi.org/10.1038/s41467-019-09982-5]

> Kaya-Okur, H. S., Wu, S. J., Codomo, C. A., Pledger, E. S., Bryson, T. D., Henikoff, J. G., Ahmad, K., & Henikoff, S. (2019). CUT&Tag for efficient epigenomic profiling of small samples and single cells. _Nature Communications_, _10_(1), 1930. https://doi.org/10.1038/s41467-019-09982-5]

The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a portable, reproducible manner. It is capable of using containerisation and package management making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process, which makes it easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules).

nextflow pull nf-core/cutandrun

```

## Pipeline Configuration Options

Trimming

consensus peaks

### Reproducibility

It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.

            "type": "object",

            "fa_icon": "fas fa-terminal",

            "description": "Define where the pipeline should find input data and save output data.",

            "required": [

                "input",

                "outdir"

            ],

            "required": ["input", "outdir"],

            "properties": {

                "input": {

                    "type": "string",

                    "description": "Method used to save pipeline results to output directory.",

                    "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",

                    "fa_icon": "fas fa-copy",

                    "enum": [

                        "symlink",

                        "rellink",

                        "link",

                        "copy",

                        "copyNoFollow",

                        "move"

                    ],

                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],

                    "hidden": true

                },

                "email_on_fail": {