nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/cutandrun/master/nextflow_schema.json",
    "title": "nf-core/cutandrun pipeline parameters",
    "description": "Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes sequencing QC, spike-in normalisation, IgG control normalisation, peak calling and downstream peak analysis.",
    "type": "object",
    "definitions": {
        "input_output_options": {
            "title": "Input/output options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "required": ["input", "outdir"],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re//usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "outdir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "The output directory where the results will be saved. You have to use absolute paths to store on Cloud infrastructure.",
                    "fa_icon": "fas fa-folder-open",
                    "default": "./results"
                },
                "multiqc_title": {
                    "type": "string",
                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                    "fa_icon": "fas fa-file-signature"
                },
                "save_reference": {
                    "type": "boolean",
                    "fa_icon": "fas fa-folder-plus",
                    "description": "Save genome reference data to the output directory"
                },
                "save_merged_fastq": {
                    "type": "boolean",
                    "fa_icon": "fas fa-folder-plus",
                    "description": "Save any technical replicate FASTQ files that were merged to the output directory"
                },
                "save_trimmed": {
                    "type": "boolean",
                    "fa_icon": "fas fa-folder-plus",
                    "description": "Save trimmed FASTQ files to the output directory"
                },
                "save_spikein_aligned": {
                    "type": "boolean",
                    "fa_icon": "fas fa-folder-plus",
                    "description": "Save BAM files aligned to the spike-in genome to the output directory"
                },
                "save_unaligned": {
                    "type": "boolean",
                    "fa_icon": "fas fa-folder-plus",
                    "description": "Save unaligned sequences to the output directory"
                },
                "save_align_intermed": {
                    "type": "boolean",
                    "fa_icon": "fas fa-folder-plus",
                    "description": "Save alignment intermediates to the output directory (WARNING: can be very large)"
                },
                "email": {
                    "type": "string",
                    "description": "Email address for completion summary.",
                    "fa_icon": "fas fa-envelope",
                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
                },
                "dump_scale_factors": {
                    "type": "boolean",
                    "description": "Output calculated scale factors from pipeline"
                }
            }
        },
        "reference_data_options": {
            "title": "Reference data options",
            "type": "object",
            "fa_icon": "fas fa-dna",
            "description": "Reference genome related files and options.",
            "properties": {
                "genome": {
                    "type": "string",
                    "description": "Name of iGenomes reference.",
                    "fa_icon": "fas fa-book",
                    "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
                },
                "bowtie2": {
                    "type": "string",
                    "fa_icon": "fas fa-book",
                    "description": "Path to bowtie2 index"
                },
                "gtf": {
                    "type": "string",
                    "fa_icon": "fas fa-book",
                    "description": "Path to GTF annotation file"
                },
                "gene_bed": {
                    "type": "string",
                    "fa_icon": "fas fa-book",
                    "description": "Path to gene BED file"
                },
                "blacklist": {
                    "type": "string",
                    "fa_icon": "fas fa-book",
                    "description": "Path to genome blacklist"
                },
                "spikein_genome": {
                    "type": "string",
                    "default": "K12-MG1655",
                    "fa_icon": "fas fa-book",
                    "description": "Name of the iGenome reference for the spike-in genome, defaulting to E. coli K12, for yeast set to R64-1-1, for fruit fly BDGP6"
                },
                "spikein_bowtie2": {
                    "type": "string",
                    "fa_icon": "fas fa-book",
                    "description": "Path to spike-in bowtie2 index"
                },
                "spikein_fasta": {
                    "type": "string",
                    "fa_icon": "fas fa-book",
                    "description": "Path to spike-in fasta"
                },
                "fasta": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
                    "description": "Path to FASTA genome file.",
                    "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
                    "fa_icon": "far fa-file-code"
                },
                "igenomes_ignore": {
                    "type": "boolean",
                    "description": "Do not load the iGenomes reference config.",
                    "fa_icon": "fas fa-ban",
                    "hidden": true,
                    "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
                }
            }
        },
        "flow_switching_options": {
            "title": "Flow switching options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "only_input": {
                    "type": "boolean",
                    "fa_icon": "fas fa-hand-paper",
                    "description": "Run pipeline up to input checking"
                },
                "only_genome": {
                    "type": "boolean",
                    "fa_icon": "fas fa-hand-paper",
                    "description": "Run pipeline up to reference preparation"
                },
                "only_preqc": {
                    "type": "boolean",
                    "fa_icon": "fas fa-hand-paper",
                    "description": "Run pipeline up to pre-alignment"
                },
                "only_alignment": {
                    "type": "boolean",
                    "fa_icon": "fas fa-hand-paper",
                    "description": "Run pipeline up to alignment"
                },
                "only_filtering": {
                    "type": "boolean",
                    "fa_icon": "fas fa-hand-paper",
                    "description": "Run pipeline up to q-filtering"
                },
                "only_peak_calling": {
                    "type": "boolean",
                    "fa_icon": "fas fa-hand-paper",
                    "description": "Run pipeline up to peak calling"
                },
                "skip_fastqc": {
                    "type": "boolean",
                    "fa_icon": "fas fa-random",
                    "description": "Skips fastqc reporting"
                },
                "skip_trimming": {
                    "type": "boolean",
                    "fa_icon": "fas fa-random",
                    "description": "Skips trimming"
                },
                "skip_removeduplicates": {
                    "type": "boolean",
                    "fa_icon": "fas fa-random",
                    "description": "Skips de-duplication"
                },
                "skip_reporting": {
                    "type": "boolean",
                    "fa_icon": "fas fa-random",
                    "description": "Skips reporting"
                },
                "skip_preseq": {
                    "type": "boolean",
                    "description": "Skips preseq reporting"
                },
                "skip_igv": {
                    "type": "boolean",
                    "fa_icon": "fas fa-random",
                    "description": "Skips igv session generation"
                },
                "skip_dt_qc": {
                    "type": "boolean",
                    "description": "Skips deeptools QC repoting",
                    "fa_icon": "fas fa-random"
                },
                "skip_heatmaps": {
                    "type": "boolean",
                    "fa_icon": "fas fa-random",
                    "description": "Skips deeptools heatmap generation"
                },
                "skip_peak_qc": {
                    "type": "boolean",
                    "description": "Skips peak QC reporting",
                    "fa_icon": "fas fa-random"
                },
                "skip_multiqc": {
                    "type": "boolean",
                    "fa_icon": "fas fa-random",
                    "description": "Skips multiqc"
                }
            },
            "fa_icon": "fas fa-exchange-alt"
        },
        "trimming_options": {
            "title": "Trimming Options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "clip_r1": {
                    "type": "integer",
                    "default": 0,
                    "fa_icon": "fas fa-align-justify",
                    "description": "Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads)."
                },
                "clip_r2": {
                    "type": "integer",
                    "default": 0,
                    "fa_icon": "fas fa-align-justify",
                    "description": "Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only)."
                },
                "three_prime_clip_r1": {
                    "type": "integer",
                    "default": 0,
                    "fa_icon": "fas fa-align-justify",
                    "description": "Instructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed."
                },
                "three_prime_clip_r2": {
                    "type": "integer",
                    "default": 0,
                    "fa_icon": "fas fa-align-justify",
                    "description": "Instructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed."
                },
                "trim_nextseq": {
                    "type": "integer",
                    "default": 0,
                    "fa_icon": "fas fa-align-justify",
                    "description": "Instructs Trim Galore to apply the --nextseq=X option, to trim based on quality after removing poly-G tails.",
                    "help_text": "This enables the option Cutadapt `--nextseq-trim=3'CUTOFF` option via Trim Galore, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored. This trimming is in common for the NextSeq- and NovaSeq-platforms, where basecalls without any signal are called as high-quality G bases."
                }
            },
            "fa_icon": "fas fa-cut"
        },
        "pipeline_options": {
            "title": "Pipeline Options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "aligner": {
                    "type": "string",
                    "default": "bowtie2",
                    "hidden": true,
                    "fa_icon": "fas fa-align-justify",
                    "description": "Select aligner"
                },
                "normalisation_c": {
                    "type": "integer",
                    "default": 10000,
                    "hidden": true,
                    "fa_icon": "fas fa-align-justify",
                    "description": "Normalisation constant for spike-in read normalisation"
                },
                "minimum_alignment_q_score": {
                    "type": "integer",
                    "default": 20,
                    "fa_icon": "fas fa-sort-numeric-down",
                    "description": "Filter reads below a q-score threshold"
                },
                "remove_mitochondrial_reads": {
                    "type": "boolean",
                    "fa_icon": "fas fa-clone",
                    "description": "Filter mitochondrial reads"
                },
                "mito_name": {
                    "type": "string",
                    "fa_icon": "fas fa-book",
                    "description": "Name of mitochondrial reads in reference genome. Only necessary when using a custom (non-igenomes) reference genome."
                },
                "dedup_target_reads": {
                    "type": "boolean",
                    "fa_icon": "fas fa-clone",
                    "description": "De-duplicate target reads AND control reads (default is control only)"
                },
                "remove_linear_duplicates": {
                    "type": "boolean",
                    "fa_icon": "fas fa-clone",
                    "description": "De-duplicate reads based on read 1 5' start position. Relevant for assays using linear amplification with tagmentation (default is false)."
                },
                "end_to_end": {
                    "type": "boolean",
                    "fa_icon": "fas fa-clone",
                    "default": true,
                    "description": "Use --end-to-end mode of Bowtie2 during alignment"
                },
                "normalisation_mode": {
                    "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"]
                },
                "normalisation_binsize": {
                    "type": "integer",
                    "default": 50,
                    "description": "If normsalisation option is one of  \"RPKM\", \"CPM\", \"BPM\" - then the binsize that the reads count is calculated on is used.",
                    "fa_icon": "fas fa-arrows-alt-h"
                },
                "peakcaller": {
                    "type": "string",
                    "default": "seacr",
                    "fa_icon": "fas fa-align-justify",
                    "description": "Selects the peak caller for the pipeline. Options are: [seacr, macs2]. More than one peak caller can be chosen and the order specifies which is a primary peak called (the first) that will be used downstream. Any secondary peak callers will be run and outputed to the results folder."
                },
                "use_control": {
                    "type": "boolean",
                    "default": true,
                    "fa_icon": "fas fa-align-justify",
                    "description": "Specifies whether to use a control to normalise peak calls against (e.g. IgG)"
                },
                "extend_fragments": {
                    "type": "boolean",
                    "default": true,
                    "fa_icon": "fas fa-align-justify",
                    "description": "Specifies whether to extend paired-end fragments between the read mates when calculating coveage tracks"
                },
                "igg_scale_factor": {
                    "type": "number",
                    "default": 0.5,
                    "fa_icon": "fas fa-align-justify",
                    "description": "Specifies whether the background control is scaled prior to being used to normalise peaks."
                },
                "seacr_peak_threshold": {
                    "type": "number",
                    "default": 0.05,
                    "fa_icon": "fas fa-align-justify",
                    "description": "SEACR specifies returns the top n fraction (between 0 and 1) of peaks based on total signal within peaks. This is only used if there are no controls included with the samples and if `--use_control` is `false`"
                },
                "seacr_norm": {
                    "type": "string",
                    "default": "non",
                    "fa_icon": "fas fa-align-justify",
                    "description": "SEACR normalization. ",
                    "enum": ["non", "norm"]
                },
                "seacr_stringent": {
                    "type": "string",
                    "default": "stringent",
                    "fa_icon": "fas fa-align-justify",
                    "description": "SEACR stringency.",
                    "enum": ["stringent", "relaxed"]
                },
                "macs2_qvalue": {
                    "type": "number",
                    "default": 0.01,
                    "fa_icon": "fas fa-align-justify",
                    "description": "Q-value threshold for MACS2 peak caller."
                },
                "macs2_pvalue": {
                    "type": "number",
                    "fa_icon": "fas fa-align-justify",
                    "description": "P-value threshold for macs2 peak caller. If set it will overide the qvalue."
                },
                "macs_gsize": {
                    "type": "number",
                    "default": 2700000000,
                    "fa_icon": "fas fa-align-justify",
                    "description": "parameter required by MACS2. If using an iGenomes reference these have been provided when `--genome` is set as *GRCh37*, *GRCh38*, *GRCm38*, *WBcel235*, *BDGP6*, *R64-1-1*, *EF2*, *hg38*, *hg19* and *mm10*. Otherwise the gsize will default to GRCh38."
                },
                "macs2_narrow_peak": {
                    "type": "boolean",
                    "default": true,
                    "fa_icon": "fas fa-align-justify",
                    "description": "Determines whether MACS2 broad or narrow peak mode is used for the peak caller"
                },
                "macs2_broad_cutoff": {
                    "type": "number",
                    "default": 0.1,
                    "fa_icon": "fas fa-align-justify",
                    "description": "MACS2 broad cutoff parameter"
                },
                "consensus_peak_mode": {
                    "type": "string",
                    "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"]
                },
                "replicate_threshold": {
                    "type": "number",
                    "default": 1,
                    "fa_icon": "fas fa-align-justify",
                    "description": "Minimum number of overlapping replicates needed for a consensus peak"
                },
                "igv_show_gene_names": {
                    "type": "boolean",
                    "default": true,
                    "fa_icon": "fas fa-align-justify",
                    "description": "Show gene names instead of symbols in IGV browser sessions"
                }
            },
            "fa_icon": "fas fa-cog"
        },
        "reporting_options": {
            "title": "Reporting Options",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-atlas",
            "properties": {
                "dt_qc_bam_binsize": {
                    "type": "integer",
                    "default": 500,
                    "description": "Deeptools multiBamSummary bam bin size",
                    "fa_icon": "fas fa-align-justify"
                },
                "dt_qc_corr_method": {
                    "type": "string",
                    "default": "pearson",
                    "description": "Deeptools Correlation Plot statistical calculation method"
                },
                "dt_heatmap_gene_beforelen": {
                    "type": "integer",
                    "default": 3000,
                    "description": "Deeptools heatmap gene plot before length (bases)",
                    "fa_icon": "fas fa-align-justify"
                },
                "dt_heatmap_gene_bodylen": {
                    "type": "integer",
                    "default": 5000,
                    "description": "Deeptools heatmap gene plot body length (bases)",
                    "fa_icon": "fas fa-align-justify"
                },
                "dt_heatmap_gene_afterlen": {
                    "type": "integer",
                    "default": 3000,
                    "description": "Deeptools heatmap gene plot after length (bases)",
                    "fa_icon": "fas fa-align-justify"
                },
                "dt_heatmap_peak_beforelen": {
                    "type": "integer",
                    "default": 3000,
                    "description": "Deeptools heatmap peak plot before length (bases)",
                    "fa_icon": "fas fa-align-justify"
                },
                "dt_heatmap_peak_afterlen": {
                    "type": "integer",
                    "default": 3000,
                    "description": "Deeptools heatmap peak plot after length (bases)",
                    "fa_icon": "fas fa-align-justify"
                },
                "dt_calc_all_matrix": {
                    "type": "boolean",
                    "default": true,
                    "description": "Flag for whether to generate a heatmap for all samples together"
                },
                "min_frip_overlap": {
                    "type": "number",
                    "default": 0.2,
                    "description": "Minimum fragment overlap for FriP score",
                    "fa_icon": "fas fa-align-justify"
                },
                "min_peak_overlap": {
                    "type": "number",
                    "default": 0.2,
                    "description": "Minimum peak overlap for peak reproducibility plot",
                    "fa_icon": "fas fa-align-justify"
                },
                "igv_sort_by_groups": {
                    "type": "boolean",
                    "default": true,
                    "description": "Sort the IGV output tracks by group"
                }
            }
        },
        "institutional_config_options": {
            "title": "Institutional config options",
            "type": "object",
            "fa_icon": "fas fa-university",
            "description": "Parameters used to describe centralised config profiles. These should not be edited.",
            "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
            "properties": {
                "custom_config_version": {
                    "type": "string",
                    "description": "Git commit id for Institutional configs.",
                    "default": "master",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "custom_config_base": {
                    "type": "string",
                    "description": "Base directory for Institutional configs.",
                    "default": "https://raw.githubusercontent.com/nf-core/configs/master",
                    "hidden": true,
                    "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_name": {
                    "type": "string",
                    "description": "Institutional config name.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_description": {
                    "type": "string",
                    "description": "Institutional config description.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_contact": {
                    "type": "string",
                    "description": "Institutional config contact information.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                },
                "config_profile_url": {
                    "type": "string",
                    "description": "Institutional config URL link.",
                    "hidden": true,
                    "fa_icon": "fas fa-users-cog"
                }
            }
        },
        "max_job_request_options": {
            "title": "Max job request options",
            "type": "object",
            "fa_icon": "fab fa-acquisitions-incorporated",
            "description": "Set the top limit for requested resources for any single job.",
            "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
            "properties": {
                "max_cpus": {
                    "type": "integer",
                    "description": "Maximum number of CPUs that can be requested for any single job.",
                    "default": 16,
                    "fa_icon": "fas fa-microchip",
                    "hidden": true,
                    "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
                },
                "max_memory": {
                    "type": "string",
                    "description": "Maximum amount of memory that can be requested for any single job.",
                    "default": "128.GB",
                    "fa_icon": "fas fa-memory",
                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
                    "hidden": true,
                    "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
                },
                "max_time": {
                    "type": "string",
                    "description": "Maximum amount of time that can be requested for any single job.",
                    "default": "240.h",
                    "fa_icon": "far fa-clock",
                    "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
                    "hidden": true,
                    "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
                }
            }
        },
        "generic_options": {
            "title": "Generic options",
            "type": "object",
            "fa_icon": "fas fa-file-import",
            "description": "Less common options for the pipeline, typically set in a config file.",
            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
            "properties": {
                "help": {
                    "type": "boolean",
                    "description": "Display help text.",
                    "fa_icon": "fas fa-question-circle",
                    "hidden": true
                },
                "version": {
                    "type": "boolean",
                    "description": "Display version and exit.",
                    "fa_icon": "fas fa-question-circle",
                    "hidden": true
                },
                "publish_dir_mode": {
                    "type": "string",
                    "default": "copy",
                    "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"],
                    "hidden": true
                },
                "singularity_pull_docker_container": {
                    "type": "boolean",
                    "description": "Pull Docker container."
                },
                "email_on_fail": {
                    "type": "string",
                    "description": "Email address for completion summary, only when pipeline fails.",
                    "fa_icon": "fas fa-exclamation-triangle",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
                    "help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
                    "hidden": true
                },
                "plaintext_email": {
                    "type": "boolean",
                    "description": "Send plain-text email instead of HTML.",
                    "fa_icon": "fas fa-remove-format",
                    "hidden": true
                },
                "max_multiqc_email_size": {
                    "type": "string",
                    "description": "File size limit when attaching MultiQC reports to summary emails.",
                    "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
                    "default": "25.MB",
                    "fa_icon": "fas fa-file-upload",
                    "hidden": true
                },
                "monochrome_logs": {
                    "type": "boolean",
                    "description": "Do not use coloured log outputs.",
                    "fa_icon": "fas fa-palette",
                    "hidden": true
                },
                "hook_url": {
                    "type": "string",
                    "description": "Incoming hook URL for messaging service",
                    "fa_icon": "fas fa-people-group",
                    "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                    "hidden": true
                },
                "multiqc_config": {
                    "type": "string",
                    "format": "file-path",
                    "description": "Custom config file to supply to MultiQC.",
                    "fa_icon": "fas fa-cog",
                    "hidden": true
                },
                "multiqc_logo": {
                    "type": "string",
                    "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
                    "fa_icon": "fas fa-image",
                    "hidden": true
                },
                "multiqc_methods_description": {
                    "type": "string",
                    "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                    "fa_icon": "fas fa-cog"
                },
                "validate_params": {
                    "type": "boolean",
                    "description": "Boolean whether to validate parameters against the schema at runtime",
                    "default": true,
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                },
                "validationShowHiddenParams": {
                    "type": "boolean",
                    "fa_icon": "far fa-eye-slash",
                    "description": "Show all params when using `--help`",
                    "hidden": true,
                    "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
                },
                "validationFailUnrecognisedParams": {
                    "type": "boolean",
                    "fa_icon": "far fa-check-circle",
                    "description": "Validation of parameters fails when an unrecognised parameter is found.",
                    "hidden": true,
                    "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
                },
                "validationLenientMode": {
                    "type": "boolean",
                    "fa_icon": "far fa-check-circle",
                    "description": "Validation of parameters in lenient more.",
                    "hidden": true,
                    "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/reference_data_options"
        },
        {
            "$ref": "#/definitions/flow_switching_options"
        },
        {
            "$ref": "#/definitions/trimming_options"
        },
        {
            "$ref": "#/definitions/pipeline_options"
        },
        {
            "$ref": "#/definitions/reporting_options"
        },
        {
            "$ref": "#/definitions/institutional_config_options"
        },
        {
            "$ref": "#/definitions/max_job_request_options"
        },
        {
            "$ref": "#/definitions/generic_options"
        }
    ]
}