nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/hicar/master/nextflow_schema.json",
    "title": "nf-core/hicar pipeline parameters",
    "description": "This pipeline analyses data for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.",
    "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",
                    "schema": "assets/schema_input.json",
                    "pattern": "^\\S+\\.(csv|tsv|yaml)$",
                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/hicar/usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "method": {
                    "type": "string",
                    "description": "Metho for the experiment.",
                    "default": "HiCAR",
                    "help_text": "It can be HiCAR, HiChIP, ChIA-PET, PLAC-Seq. If it is not HiCAR, user may want to define the anchor peaks. Otherwise, the anchor peaks will be called by R2 reads.",
                    "fa_icon": "fas fa-atom"
                },
                "anchor_peaks": {
                    "type": "string",
                    "format": "file-path",
                    "pattern": "^\\S+\\.(narrowPeak|boradPeak)$",
                    "description": "Path to anchor peaks",
                    "help_text": "The anchor peaks can be a narrowPeak or broadPeak.",
                    "fa_icon": "fab fa-think-peaks"
                },
                "outdir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                    "fa_icon": "fas fa-folder-open"
                },
                "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})$"
                },
                "multiqc_title": {
                    "type": "string",
                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                    "fa_icon": "fas fa-file-signature"
                }
            }
        },
        "reference_genome_options": {
            "title": "Reference genome options",
            "type": "object",
            "fa_icon": "fas fa-dna",
            "description": "Reference genome related files and options required for the workflow.",
            "properties": {
                "genome": {
                    "type": "string",
                    "description": "Name of iGenomes reference.",
                    "fa_icon": "fas fa-book",
                    "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
                },
                "fasta": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
                    "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_base": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Directory / URL base for iGenomes references.",
                    "default": "s3://ngi-igenomes/igenomes",
                    "fa_icon": "fas fa-cloud-download-alt",
                    "hidden": true
                },
                "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`."
                },
                "bwa_index": {
                    "type": "string",
                    "exists": true,
                    "fa_icon": "fab fa-wpexplorer",
                    "description": "Path to bwa index file.",
                    "help_text": "If you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible."
                },
                "gtf": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "fa_icon": "fas fa-map-marked-alt",
                    "description": "Path to annotation gtf file.",
                    "help_text": "Annotation gtf or gff file is required for annotation and quality control. This parameter is *mandatory* if `--genome` is not specified."
                },
                "gff": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "fa_icon": "fas fa-map-marked-alt",
                    "description": "Path to annotation gff file.",
                    "help_text": "Annotation gff or gff file is required for annotation and quality control. This parameter is *mandatory* if `--genome` is not specified."
                },
                "gene_bed": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "fa_icon": "fas fa-file-medical-alt",
                    "description": "Path to annotation gene bed file.",
                    "help_text": "Path to BED file containing gene intervals. This will be created from the GTF file if not specified."
                },
                "mappability": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "fa_icon": "fas fa-file-contract",
                    "description": "Path to genome mappability file.",
                    "help_text": "If you have no genome mappability available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible."
                },
                "macs_gsize": {
                    "type": "string",
                    "description": "Effective genome size parameter required by MACS2.",
                    "help_text": "[Effective genome size](https://github.com/taoliu/MACS#-g--gsize) 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*. For other genomes, if this parameter is not specified then the MACS2 peak-calling and differential analysis will be skipped.",
                    "fa_icon": "fas fa-arrows-alt-h"
                },
                "ucscname": {
                    "type": "string",
                    "description": "UCSC assembly annotation name.",
                    "help_text": "[UCSC assembly annotation name](https://genome.ucsc.edu/FAQ/FAQgenes.html)",
                    "fa_icon": "fas fa-water"
                },
                "blacklist": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "description": "Path to blacklist regions in BED format, used for filtering alignments.",
                    "help_text": "If provided, alignments that overlap with the regions in this file will be filtered out (see [ENCODE blacklists](https://sites.google.com/site/anshulkundaje/projects/blacklists)). The file should be in BED format. Blacklisted regions for *GRCh37*, *GRCh38*, *GRCm38*, *hg19*, *hg38*, *mm10* are bundled with the pipeline in the [`blacklists`](../assets/blacklists/) directory, and as such will be automatically used if any of those genomes are specified with the `--genome` parameter.",
                    "fa_icon": "fas fa-book-dead"
                },
                "publish_mappability": {
                    "type": "boolean",
                    "description": "publish mappability to results genome/mappability folder",
                    "fa_icon": "fas fa-align-center"
                },
                "publish_genome": {
                    "type": "boolean",
                    "description": "publish genome",
                    "fa_icon": "fas fa-dna"
                }
            }
        },
        "experiment_config_options": {
            "title": "Experiment design options",
            "type": "object",
            "fa_icon": "fas fa-vials",
            "description": "Parameters used to describe the experiment designs.",
            "properties": {
                "enzyme": {
                    "type": "string",
                    "description": "Specifies that the cutting position has to be using.",
                    "fa_icon": "fas fa-vial",
                    "help_text": "Default CviQI digestion. Available enzymes are MboI, DpnII, BglII, HindIII, MseI, and CviQI.",
                    "default": "CviQI"
                },
                "restriction_sites": {
                    "type": "string",
                    "description": "Specifies that the cutting sequence has to be using.",
                    "fa_icon": "fas fa-cut",
                    "help_text": "It will be automatically assigned by the enzyme inputed.",
                    "hidden": true,
                    "default": "^TAC"
                },
                "restriction_sites_cut_off": {
                    "type": "number",
                    "description": "Specifies that the cutoff value used for mappability filter.",
                    "fa_icon": "fas fa-ruler-horizontal",
                    "help_text": "Default is 0.5. It is the average over just covered bases.",
                    "hidden": false,
                    "default": 0.5
                },
                "cutadapt_5end": {
                    "type": "string",
                    "description": "trim 5' end with the string if not skip_cutadapt",
                    "fa_icon": "fas fa-remove-format",
                    "hidden": false,
                    "default": "^TAC"
                }
            }
        },
        "MACS2_peak_calling_options": {
            "title": "MACS2 peak calling options",
            "type": "object",
            "fa_icon": "fas fa-mountains",
            "descripton": "Options for MACS2 peak calling options for ATAC-seq reads (R2).",
            "properties": {
                "shiftsize": {
                    "type": "integer",
                    "description": "shift size for MACS2",
                    "fa_icon": "fas fa-arrows-alt-h",
                    "hidden": false,
                    "help_text": "How reads will be shift to increase the peak/noise ratios. See help from [MACS2 documentation](https://github.com/macs3-project/MACS/blob/master/docs/callpeak.md)",
                    "default": -75
                },
                "smooth_window": {
                    "type": "integer",
                    "description": "extsize for MACS2",
                    "fa_icon": "fas fa-compress",
                    "hidden": false,
                    "help_text": "How reads will be extend in 5'->3' direction to increase the fragment size. See help from [MACS2 documentation](https://github.com/macs3-project/MACS/blob/master/docs/callpeak.md)",
                    "default": 150
                },
                "qval_thresh": {
                    "type": "number",
                    "description": "cutoff qvalue",
                    "fa_icon": "fas fa-filter",
                    "hidden": false,
                    "help_text": "The minimum FDR cutoff to call significant peak for R2 reads. See help from [MACS2 documentation](https://github.com/macs3-project/MACS/blob/master/docs/callpeak.md)",
                    "default": 0.01
                }
            }
        },
        "loops_calling_options": {
            "title": "Interactions calling options",
            "type": "object",
            "fa_icon": "fab fa-connectdevelop",
            "descripton": "Options for loops calling options.",
            "properties": {
                "cool_bin": {
                    "type": "string",
                    "description": "resolution bin size",
                    "fa_icon": "fas fa-layer-group",
                    "hidden": false,
                    "help_text": "Bin size for singal resampling.",
                    "default": "5000_10000"
                },
                "maps_digest_file": {
                    "type": "string",
                    "description": "output of restriction_cut_multipleenzyme.py.",
                    "help_text": "See https://github.com/ijuric/MAPS/blob/master/bin/utils/genomic_features_generator/scripts/restriction_cut_multipleenzyme.py.",
                    "default": "None",
                    "hidden": false,
                    "fa_icon": "fas fa-stream"
                },
                "maps_cutoff_counts": {
                    "type": "integer",
                    "description": "MAPS regression cutoff value",
                    "fa_icon": "fas fa-filter",
                    "hidden": false,
                    "help_text": "Minimal cutoff value for coverage in the called connections. See help from [MAPS documentation](https://github.com/ijuric/MAPS), default 12.",
                    "default": 12
                },
                "maps_cutoff_fold_change": {
                    "type": "number",
                    "description": "MAPS regression fold change cutoff value",
                    "fa_icon": "fas fa-check-double",
                    "hidden": false,
                    "help_text": "Miniaml cutoff value for fold change from signal to expected values. See help from [MAPS documentation](https://github.com/ijuric/MAPS), default 2.",
                    "default": 2.0
                },
                "maps_cutoff_fdr": {
                    "type": "number",
                    "description": "MAPS regression -log10(fdr) cutoff value",
                    "fa_icon": "fas fa-percent",
                    "hidden": false,
                    "help_text": "Minimal cutoff -log10(FDR) value in the called connections. See help from [MAPS documentation](https://github.com/ijuric/MAPS), default 2 (=fdr 0.01).",
                    "default": 2.0
                },
                "maps_filter": {
                    "type": "string",
                    "description": "MAPS regression filter file name",
                    "fa_icon": "fas fa-clipboard",
                    "hidden": false,
                    "help_text": "file containing bins that need to be filtered out. Format: two columns 'chrom', 'bin'. 'chrom' contains 'chr1','chr2',.. 'bin' is bin label",
                    "default": "None"
                },
                "maps_model": {
                    "type": "string",
                    "description": "MAPS regression type",
                    "fa_icon": "fas fa-cogs",
                    "hidden": false,
                    "help_text": "pospoisson for positive poisson regression, negbinom for negative binomial. default is pospoisson.",
                    "default": "pospoisson",
                    "enum": ["pospoisson", "negbinom"]
                },
                "remove_dup": {
                    "type": "boolean",
                    "description": "remove duplicates for high resolution peaks or not",
                    "fa_icon": "fas fa-mountain",
                    "hidden": true
                },
                "snow_type": {
                    "type": "string",
                    "description": "Type of snow cluster to use",
                    "help_text": "Possible values are 'SOCK' (default), 'MPI' and 'FORK'. This will be used by snow package for HiPeak calling",
                    "fa_icon": "fas fa-network-wired",
                    "hidden": false,
                    "default": "SOCK"
                },
                "peak_pair_block": {
                    "type": "number",
                    "description": "The block number of peak pair",
                    "help_text": "The block number of peak pair in each thread to count the reads. Smaller number will decrease the memory cost and increase the computation time for parepare the counts in hipeak calling.",
                    "fa_icon": "fas fa-th",
                    "hidden": true,
                    "default": 1000000000
                },
                "min_counts_per_loop": {
                    "type": "integer",
                    "description": "The minimal number reads count of peak pair",
                    "fa_icon": "fas fa-th",
                    "hidden": true,
                    "default": 1
                },
                "create_maps_signal": {
                    "type": "boolean",
                    "description": "create cooler files for MAPS or not",
                    "fa_icon": "fas fa-comment-slash",
                    "hidden": true
                },
                "hicdcplus_cutoff_fdr": {
                    "type": "number",
                    "description": "FDR cutoff value",
                    "fa_icon": "fas fa-percent",
                    "hidden": false,
                    "help_text": "Minimal cutoff FDR value in the called connections. See help from [HiCDCPlus documentation](https://bioconductor.org/packages/HiCDCPlus/), default 0.05.",
                    "default": 0.05
                },
                "peakachu_pretrained_url": {
                    "type": "string",
                    "description": "The predefined modle download prefix string",
                    "fa_icon": "fas fa-percent",
                    "hidden": false,
                    "help_text": "This method is only available for HiCAR data.",
                    "default": "http://3dgenome.fsm.northwestern.edu/peakachu/HiCAR-models/HiCAR-peakachu-pretrained."
                },
                "call_high_peak": {
                    "type": "boolean",
                    "description": "Call high resolution peaks or not",
                    "fa_icon": "fas fa-mountain",
                    "hidden": false
                },
                "r1_pval_thresh": {
                    "type": "number",
                    "description": "cutoff pvalue for fragment (R1)",
                    "fa_icon": "fas fa-filter",
                    "hidden": false,
                    "help_text": "The minimum FDR cutoff to call significant peak for R1 reads. R1 reads will be more noisy compare to R2 reads. Here we need a loose cutoff. And this will be fixed in the following steps.",
                    "default": 0.1
                }
            }
        },
        "compartment_tads_apa_options": {
            "title": "Options related to compartment, TADs calling, and APA",
            "type": "object",
            "fa_icon": "fab fa-wpforms",
            "descripton": "Options for compartment, TADs calling, and APA",
            "properties": {
                "res_compartments": {
                    "type": "integer",
                    "description": "The resolution for compartments calling",
                    "fa_icon": "fas fa-th",
                    "default": 100000
                },
                "res_tads": {
                    "type": "integer",
                    "description": "The resolution for TADs calling",
                    "help_text": "If tad_tool is set to resolution, the windows will be calculated by 3X, 5X, 10X and 15X resolution. If tad_tool is set to hicfindtads, this will determine the step parameter.",
                    "fa_icon": "fas fa-th",
                    "default": 10000
                },
                "tad_tool": {
                    "type": "string",
                    "description": "The caller for TADs, available choices: 'cooltools', 'hicexplorer', 'homer'",
                    "help_text": "Possible tools are hicfindtads and cooltools (by insulation function).",
                    "fa_icon": "fas fa-th",
                    "default": "hicexplorer",
                    "enum": ["cooltools", "hicexplorer", "homer"]
                },
                "apa_peak": {
                    "type": "string",
                    "description": "The APA peak path",
                    "default": "Anchor 1D peaks",
                    "hidden": false,
                    "fa_icon": "fas fa-caret-up"
                },
                "apa_tool": {
                    "type": "string",
                    "default": "hicexplorer",
                    "description": "APA tool, available choices: 'cooltools', 'hicexplorer', and 'juicebox'",
                    "fa_icon": "fab fa-adn",
                    "enum": ["cooltools", "hicexplorer", "juicebox"]
                },
                "apa_format": {
                    "type": "string",
                    "description": "The APA output figure format. Currently this parameter will not affect the Juicer output format (always png format).",
                    "default": "png",
                    "hidden": false,
                    "fa_icon": "fas fa-caret-up"
                },
                "compartments_tool": {
                    "type": "string",
                    "default": "cooltools",
                    "description": "Call compartment tool, available choices: 'cooltools', 'hicexplorer', 'homer', and 'juicebox'",
                    "fa_icon": "fas fa-expand",
                    "enum": ["cooltools", "hicexplorer", "homer", "juicebox"]
                },
                "interactions_tool": {
                    "type": "string",
                    "default": "maps",
                    "description": "Call loops tool, available choices: 'maps', 'hicdcplus', and 'peakachu'",
                    "fa_icon": "fab fa-airbnb",
                    "enum": ["maps", "hicdcplus", "peakachu"]
                },
                "da_tool": {
                    "type": "string",
                    "default": "diffhic",
                    "description": "Differential analysis tool. Possible options are 'edger', 'diffhic', 'hicexplorer', and 'setOperation'",
                    "fa_icon": "fas fa-adjust",
                    "enum": ["edger", "diffhic", "hicexplorer", "setOperation"]
                },
                "v4c_tool": {
                    "type": "string",
                    "default": "hicexplorer",
                    "description": "virtual 4c tool, available choices: 'cooltools', 'hicexplorer', and 'trackviewer'",
                    "fa_icon": "fas fa-mountain",
                    "enum": ["cooltools", "hicexplorer", "trackviewer"]
                },
                "tfea_tool": {
                    "type": "string",
                    "default": "homer",
                    "fa_icon": "fas fa-infinity",
                    "description": "Transcription Factor Enrichment Analysis tool, available choices: 'atacseqtfea', and 'homer'",
                    "enum": ["atacseqtfea", "homer"]
                },
                "juicer_tools_jar": {
                    "type": "string",
                    "default": "https://github.com/aidenlab/JuicerTools/releases/download/v3.0.0/juicer_tools.3.0.0.jar",
                    "description": "juicer_tools jar file url",
                    "help_text": "The juicer_tools is ued for downstream analysis such as apa/arrowhead/hiccups. The juicer_tools can be downloaded from [juicer_tools download page](https://github.com/aidenlab/JuicerTools/releases/)",
                    "fa_icon": "fab fa-java"
                },
                "juicer_norm_method": {
                    "type": "string",
                    "default": "SCALE",
                    "description": "Normalization methods",
                    "help_text": "See more details at [addNorm](https://github.com/aidenlab/juicer/wiki/AddNorm). Avaiable selection are limited by APA and Eigenvector normalization methods.",
                    "fa_icon": "fab fa-java",
                    "enum": ["VC", "VC_SQRT", "KR", "SCALE", "NONE"]
                },
                "peak_interactions_threshold": {
                    "type": "integer",
                    "default": 2,
                    "description": "parameter for HiCExplorer ChicSignificantinterations",
                    "fa_icon": "fas fa-filter"
                },
                "maps_3d_ext": {
                    "type": "string",
                    "default": "sig3Dinteractions.pe.txt",
                    "hidden": true,
                    "description": "extension file name for MAPS",
                    "fa_icon": "far fa-file"
                },
                "long_bedpe_postfix": {
                    "type": "string",
                    "default": "long.bedpe",
                    "hidden": true,
                    "description": "extension file name for long pairs",
                    "fa_icon": "far fa-file"
                },
                "short_bed_postfix": {
                    "type": "string",
                    "default": "shrt.vip.bed",
                    "hidden": true,
                    "description": "extension file name for short pairs",
                    "fa_icon": "far fa-file"
                }
            }
        },
        "Visualization_options": {
            "title": "Options related to tracks, HiCTools, and circos",
            "type": "object",
            "fa_icon": "fab fa-wpforms",
            "description": "Options for tracks viewed by igv, ucsc genome browser and virtual 4c plot tools",
            "properties": {
                "v4c_max_events": {
                    "type": "integer",
                    "description": "max events to plot for virtual 4c",
                    "fa_icon": "fas fa-water",
                    "hidden": false,
                    "default": 25
                },
                "hic_tools_jar": {
                    "type": "string",
                    "description": "The HiCTools path",
                    "default": "https://github.com/aidenlab/HiCTools/releases/download/v3.30.00/hic_tools.3.30.00.jar",
                    "fa_icon": "far fa-java",
                    "hidden": false,
                    "help_text": "This tool is used for pre/addNorm/eigenvector/pearsons/sum. Pre is the tool to create .hic file; eigenvector is used for compartment caller. The hic_tools can be downloaded from [HiCTools download page](https://github.com/aidenlab/HiCTools/releases)"
                }
            }
        },
        "Other_options_not_expose_yet": {
            "title": "Other options not expose",
            "type": "object",
            "fa_icon": "fas fa-ban",
            "hidden": true,
            "descripton": "Options under development.",
            "properties": {
                "skip_peak_qc": {
                    "type": "boolean",
                    "description": "skip peak QC or not",
                    "fa_icon": "fas fa-ban",
                    "hidden": true
                },
                "skip_plot_profile": {
                    "type": "boolean",
                    "description": "skip plot profile or not",
                    "fa_icon": "fas fa-ban",
                    "hidden": true
                },
                "skip_igv": {
                    "type": "boolean",
                    "description": "skip creat IGV files or not",
                    "fa_icon": "fas fa-ban",
                    "hidden": true
                },
                "skip_trackhub": {
                    "type": "boolean",
                    "description": "skip create trackhub files or not",
                    "fa_icon": "fas fa-ban",
                    "hidden": true
                },
                "enrichment_fdr": {
                    "type": "number",
                    "description": "cutoff value for false discovery rate of enrichment analysis",
                    "fa_icon": "fas fa-ban",
                    "hidden": true
                }
            }
        },
        "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": "fas fa-server",
            "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
                },
                "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)."
                }
            }
        },
        "pipeline_controls": {
            "title": "Pipeline controler",
            "type": "object",
            "fa_icon": "fas fa-file-import",
            "description": "To skip some processes or workflows.",
            "help_text": "These options allow you to customise some of the pipeline steps for how the pipeline runs.",
            "properties": {
                "skip_cutadapt": {
                    "type": "boolean",
                    "description": "skip trim 5'end",
                    "fa_icon": "fas fa-remove-format",
                    "hidden": false
                },
                "resample_pairs": {
                    "type": "boolean",
                    "description": "resample the pairs by pairtools",
                    "fa_icon": "fas fa-remove-format",
                    "hidden": false
                },
                "skip_fastqc": {
                    "type": "boolean",
                    "description": "skip fastqc or not",
                    "fa_icon": "fab fa-creative-commons-pd",
                    "hidden": false
                },
                "skip_peak_annotation": {
                    "type": "boolean",
                    "description": "skip peak annotation or not",
                    "fa_icon": "fas fa-comment-slash",
                    "hidden": false
                },
                "skip_diff_analysis": {
                    "type": "boolean",
                    "description": "skip differential analysis or not",
                    "fa_icon": "fas fa-ban",
                    "hidden": false
                },
                "skip_multiqc": {
                    "type": "boolean",
                    "description": "skip multiqc or not",
                    "fa_icon": "far fa-calendar-times",
                    "hidden": false
                },
                "do_apa": {
                    "type": "boolean",
                    "description": "run APA or not",
                    "fa_icon": "far fa-times-circle"
                },
                "skip_compartments": {
                    "type": "boolean",
                    "description": "skip call compartment or not",
                    "fa_icon": "far fa-comment-slash",
                    "hidden": false
                },
                "skip_tads": {
                    "type": "boolean",
                    "description": "skip call TADs or not",
                    "fa_icon": "far fa-comment-slash",
                    "hidden": false
                },
                "skip_interactions": {
                    "type": "boolean",
                    "description": "skip call interactions/loops",
                    "fa_icon": "far fa-times-circle"
                },
                "do_tfea": {
                    "type": "boolean",
                    "fa_icon": "far fa-times-circle",
                    "description": "Do Transcription Factor Enrichment Analysis or not"
                },
                "create_virtual_4c": {
                    "type": "boolean",
                    "description": "create track files for virtual 4c or not",
                    "fa_icon": "fas fa-align-left",
                    "hidden": false
                },
                "skip_circos": {
                    "type": "boolean",
                    "fa_icon": "far fa-times-circle",
                    "description": "skip circos plot"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/reference_genome_options"
        },
        {
            "$ref": "#/definitions/experiment_config_options"
        },
        {
            "$ref": "#/definitions/MACS2_peak_calling_options"
        },
        {
            "$ref": "#/definitions/loops_calling_options"
        },
        {
            "$ref": "#/definitions/compartment_tads_apa_options"
        },
        {
            "$ref": "#/definitions/Visualization_options"
        },
        {
            "$ref": "#/definitions/Other_options_not_expose_yet"
        },
        {
            "$ref": "#/definitions/institutional_config_options"
        },
        {
            "$ref": "#/definitions/max_job_request_options"
        },
        {
            "$ref": "#/definitions/generic_options"
        },
        {
            "$ref": "#/definitions/pipeline_controls"
        }
    ]
}