{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/rnafusion/master/nextflow_schema.json",
    "title": "nf-core/rnafusion pipeline parameters",
    "description": "Nextflow rnafusion analysis pipeline, part of the nf-core community.",
    "type": "object",
    "definitions": {
        "skip_steps": {
            "title": "Skip steps",
            "type": "object",
            "description": "Skip analysis steps",
            "default": "",
            "properties": {
                "skip_qc": {
                    "type": "boolean",
                    "description": "Skip QC steps"
                },
                "skip_vis": {
                    "type": "boolean",
                    "description": "Skip visualisation steps"
                }
            },
            "fa_icon": "fas fa-fast-forward"
        },
        "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": ["genomes_base", "outdir"],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/rnafusion/usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "outdir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                    "fa_icon": "fas fa-folder-open"
                },
                "email": {
                    "type": "string",
                    "description": "Email address for completion summary.",
                    "fa_icon": "fas fa-envelope",
                    "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                    "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
                },
                "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"
                },
                "build_references": {
                    "type": "boolean",
                    "fa_icon": "far fa-file-code",
                    "description": "Specifies which analysis type for the pipeline - either build references or analyse data"
                },
                "genomes_base": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to reference folder"
                },
                "ensembl_version": {
                    "type": "integer",
                    "fa_icon": "far fa-file-code",
                    "description": "ensembl version",
                    "default": 105
                },
                "starfusion_build": {
                    "type": "boolean",
                    "fa_icon": "far fa-file-code",
                    "description": "If set, starfusion references are built from scratch instead of downloaded (default)"
                },
                "read_length": {
                    "type": "integer",
                    "fa_icon": "far fa-file-code",
                    "description": "Read length",
                    "default": 100
                },
                "all": {
                    "type": "boolean",
                    "fa_icon": "far fa-file-code",
                    "description": "Build or run all references/analyses"
                },
                "arriba": {
                    "type": "boolean",
                    "fa_icon": "far fa-file-code",
                    "description": "Build or run arriba references/analyses"
                },
                "arriba_ref": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to arriba references"
                },
                "arriba_ref_blacklist": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to arriba reference blacklist"
                },
                "arriba_ref_cytobands": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to arriba reference cytobands"
                },
                "arriba_ref_known_fusions": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to arriba reference known fusions"
                },
                "arriba_ref_protein_domains": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to arriba reference protein domain"
                },
                "arriba_fusions": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to arriba output"
                },
                "ensembl_ref": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to ensembl references"
                },
                "fusioncatcher": {
                    "type": "boolean",
                    "fa_icon": "far fa-file-code",
                    "description": "Build or run fusioncatcher references/analyses"
                },
                "fusioncatcher_fusions": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to fusioncatcher output"
                },
                "fusioncatcher_limitSjdbInsertNsj": {
                    "type": "integer",
                    "fa_icon": "far fa-file-code",
                    "description": "Use limitSjdbInsertNsj with int for fusioncatcher"
                },
                "fusioncatcher_ref": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to fusioncatcher references"
                },
                "fusioninspector_filter": {
                    "type": "boolean",
                    "fa_icon": "far fa-file-code",
                    "description": "Feed filtered fusionreport fusions to fusioninspector"
                },
                "fusioninspector_limitSjdbInsertNsj": {
                    "type": "integer",
                    "fa_icon": "far fa-file-code",
                    "description": "Use limitSjdbInsertNsj with int for fusioninspector STAR process"
                },
                "fusioninspector_only": {
                    "type": "boolean",
                    "fa_icon": "far fa-file-code",
                    "description": "Skip fusion-report. --fusioninspector_fusions PATH needed to provide a fusion list as input"
                },
                "fusioninspector_fusions": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to a fusion list file built with format GENE1--GENE2"
                },
                "fusionreport": {
                    "type": "boolean",
                    "fa_icon": "far fa-file-code",
                    "description": "Build fusionreport references"
                },
                "fusionreport_ref": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to fusionreport references"
                },
                "fusionreport_filter": {
                    "type": "boolean",
                    "fa_icon": "far fa-file-code",
                    "default": true,
                    "description": "Display fusions identified with 2 tools or more"
                },
                "pizzly": {
                    "type": "boolean",
                    "fa_icon": "far fa-file-code",
                    "description": "Build or run pizzly references/analyses"
                },
                "pizzly_fusions": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to pizzly output"
                },
                "pizzly_ref": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to pizzly references"
                },
                "squid": {
                    "type": "boolean",
                    "fa_icon": "far fa-file-code",
                    "description": "Build or run squid references/analyses"
                },
                "squid_fusions": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to squid output"
                },
                "squid_ref": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to squid references"
                },
                "starfusion": {
                    "type": "boolean",
                    "fa_icon": "far fa-file-code",
                    "description": "Build or run starfusion references/analyses"
                },
                "starfusion_fusions": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to starfusion output"
                },
                "starfusion_ref": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to starfusion references"
                },
                "starindex": {
                    "type": "boolean",
                    "fa_icon": "far fa-file-code",
                    "description": "Build or run starindex references/analyses"
                },
                "starindex_ref": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to starindex references"
                },
                "stringtie": {
                    "type": "boolean",
                    "fa_icon": "far fa-file-code",
                    "description": "Run stringtie analysis"
                },
                "whitelist": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "Path to fusions to add to the input of fusioninspector"
                },
                "cosmic_username": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "COSMIC username"
                },
                "cosmic_passwd": {
                    "type": "string",
                    "fa_icon": "far fa-file-code",
                    "description": "COSMIC password"
                },
                "qiagen": {
                    "type": "boolean",
                    "fa_icon": "far fa-file-code",
                    "description": "Use QIAGEN instead of SANGER to download COSMIC database"
                }
            }
        },
        "read_trimming_options": {
            "title": "Read trimming options",
            "type": "object",
            "fa_icon": "fas fa-cut",
            "description": "Options to adjust read trimming criteria.",
            "properties": {
                "trim": {
                    "type": "boolean",
                    "description": "Preform trimming of reads, default: false",
                    "fa_icon": "fas fa-cut"
                },
                "fastp_trim": {
                    "type": "boolean",
                    "description": "Preform fastp trimming of reads, default: false",
                    "fa_icon": "fas fa-cut"
                },
                "trim_tail": {
                    "type": "integer",
                    "description": "Preform tail trimming of reads, default: null",
                    "fa_icon": "fas fa-cut"
                },
                "adapter_fasta": {
                    "type": "string",
                    "description": "Path to adapter fasta file: default: []",
                    "fa_icon": "fas fa-cut"
                }
            }
        },
        "compression_options": {
            "title": "Alignment compression options",
            "type": "object",
            "fa_icon": "fas fa-cut",
            "description": "Option to compress BAM files to CRAM.",
            "properties": {
                "cram": {
                    "type": "string",
                    "description": "List of tools for which to compress BAM file to CRAM,default: [], options: arriba, squid, starfusion. Leave no space between options",
                    "fa_icon": "fas fa-cut"
                }
            }
        },
        "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"
                },
                "fasta": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
                    "description": "Path to FASTA genome file.",
                    "fa_icon": "far fa-file-code"
                },
                "fai": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.fn?ai(\\.gz)?$",
                    "description": "Path to FASTA genome index file.",
                    "fa_icon": "far fa-file-code"
                },
                "gtf": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.gtf?(\\.gz)?$",
                    "description": "Path to GTF genome file.",
                    "fa_icon": "far fa-file-code"
                },
                "chrgtf": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.gtf?(\\.gz)?$",
                    "description": "Path to GTF genome file.",
                    "fa_icon": "far fa-file-code"
                },
                "transcript": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
                    "description": "Path to GTF genome file.",
                    "fa_icon": "far fa-file-code"
                },
                "refflat": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.refflat?$",
                    "description": "Path to GTF genome file.",
                    "fa_icon": "far fa-file-code"
                },
                "rrna_intervals": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.interval_list?$",
                    "description": "Path to ribosomal interval list.",
                    "fa_icon": "far fa-file-code"
                }
            }
        },
        "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",
                    "default": false,
                    "hidden": true
                },
                "version": {
                    "type": "boolean",
                    "description": "Display version and exit.",
                    "fa_icon": "fas fa-question-circle",
                    "default": false,
                    "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",
                    "default": false,
                    "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",
                    "default": false,
                    "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`",
                    "default": false,
                    "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.",
                    "default": false,
                    "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.",
                    "default": false,
                    "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)."
                },
                "seq_center": {
                    "type": "string",
                    "description": "Sequencing center",
                    "hidden": true,
                    "fa_icon": "fas fa-toolbox",
                    "help_text": "This will reported in the BAM header as CN"
                },
                "seq_platform": {
                    "type": "string",
                    "description": "Sequencing platform",
                    "hidden": true,
                    "fa_icon": "fas fa-toolbox",
                    "help_text": "This will reported in the BAM header as PL."
                },
                "star_ignore_sjdbgtf": {
                    "type": "boolean",
                    "description": "Whether to ignore the GTF in STAR alignment",
                    "hidden": true,
                    "fa_icon": "fas fa-toolbox",
                    "help_text": "Setting false will use GTF file for STAR alignment"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/skip_steps"
        },
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/read_trimming_options"
        },
        {
            "$ref": "#/definitions/compression_options"
        },
        {
            "$ref": "#/definitions/reference_genome_options"
        },
        {
            "$ref": "#/definitions/institutional_config_options"
        },
        {
            "$ref": "#/definitions/max_job_request_options"
        },
        {
            "$ref": "#/definitions/generic_options"
        }
    ]
}
