Prettier updates

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

- [bedtools](https://bedtools.readthedocs.io/en/latest/)

- [samtools](http://www.htslib.org/)

  > Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H, Twelve years of SAMtools and BCFtools, GigaScience (2021) 10(2) giab008.

- [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml)

  > Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359 (2012). https://doi.org/10.1038/nmeth.1923.

- [deeptools](https://deeptools.readthedocs.io/en/develop/)

  > Ramírez, Fidel, Devon P. Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S. Richter, Steffen Heyne, Friederike Dündar, and Thomas Manke. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016). doi:10.1093/nar/gkw257.

- [seacr](https://github.com/FredHutch/SEACR)

  > Meers, M.P., Tenenbaum, D. & Henikoff, S. Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling. Epigenetics & Chromatin 12, 42 (2019). https://doi.org/10.1186/s13072-019-0287-4.

- [macs2](https://github.com/macs3-project/MACS)

            "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",

                    "default": "Spikein",

                    "fa_icon": "fab fa-buffer",

                    "description": "Sets the target read normalisation mode. Options are: [\"Spikein\", \"RPKM\", \"CPM\", \"BPM\", \"None\" ]",

                    "enum": [

                        "Spikein",

                        "RPKM",

                        "CPM",

                        "BPM",

                        "None"

                    ]

                    "enum": ["Spikein", "RPKM", "CPM", "BPM", "None"]

                },

                "normalisation_binsize": {

                    "type": "integer",

                    "default": "group",

                    "fa_icon": "fas fa-align-justify",

                    "description": "Specifies what samples to group together for consensus peaks. Options are [group, all]",

                    "enum": [

                        "group",

                        "all"

                    ]

                    "enum": ["group", "all"]

                },

                "replicate_threshold": {

                    "type": "number",

                    "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": {