{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
    "title": ". pipeline parameters",
    "description": "",
    "type": "object",
    "definitions": {
        "basic_input_output_options": {
            "title": "Basic Input/Output Options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "properties": {
                "out_dir": {
                    "type": "string",
                    "default": "output",
                    "description": "Directory for output of all user-facing files."
                },
                "fastq": {
                    "type": "string",
                    "description": "Directory containing fastq input files. May contain fastq files directly or directories name barcodeXX relating to independent samples."
                },
                "sample": {
                    "type": "string",
                    "description": "A sample name for non-multiplexed data. Permissible if passing a file or directory of .fastq(.gz)."
                },
                "sample_sheet": {
                    "type": "string",
                    "description": "CSV file with columns named `barcode`, `sample_name` and `type`. Permissible if passing a directory containing barcodeXX sub-directories."
                },
                "sanitize_fastq": {
                    "type": "boolean",
                    "description": "Use additional heuristics to identify barcodes from file paths.",
                    "help_text": "Enabling this option will group together files into samples by the presence of strings of the form `barcodeXXX` present in filenames, rather than simply files grouped into directories (as output by MinKNOW and the Guppy basecaller)."
                },
                "plot_gffcmp_stats": {
                    "type": "boolean",
                    "description": "Create a pdf of plots from showing gffcompare results"
                },
                "gffcompare_opts": {
                    "type": "string",
                    "description": "Extra options for gffcompare -r",
                    "default": " -R "
                },
                "ref_genome": {
                    "type": "string",
                    "description": "Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]"
                },
                "ref_annotation": {
                    "type": "string",
                    "description": "A reference annotation of gff format"
                },
                "use_pychopper": {
                    "type": "boolean",
                    "description": "Use pychopper to preprcess reads",
                    "default": true
                },
                "pychopper_opts": {
                    "type": "string",
                    "description": "Extra pychopper opts"
                },
                "threads": {
                    "type": "integer",
                    "default": 8
                },
                "minimap_index_opts": {
                    "type": "string",
                    "description": "minimap2 extra indexing options.",
                    "default": "-k14"
                },
                "minimap2_opts": {
                    "type": "string",
                    "description": "minimap2 extra mapping options.",
                    "default": "-uf"
                },
                "minimum_mapping_quality": {
                    "type": "integer",
                    "description": "filter aligned reads by MAPQ quality.",
                    "default": 40
                },
                "poly_context": {
                    "type": "integer",
                    "description": "Region size at end of reads to apply poly(A) filter.",
                    "default": 24
                },
                "max_poly_run": {
                    "type": "integer",
                    "description": "Max poly(A) region allowed with poly_context-sized end regions.",
                    "default": 8
                },
                "bundle_min_reads": {
                    "type": "integer",
                    "description": "Minimum size of bam bundle for parallel processing."
                },
                "use_guide_annotation": {
                    "type": "boolean",
                    "description": "Use reference annotation in stringtie transcript assembly.",
                    "default": "true"
                },
                "stringtie_opts": {
                    "type": "string",
                    "description": "Extra options for stringtie transcript assembly.",
                    "default": " --conservative "
                },
                "disable_ping": {
                "type": "boolean"
                }
            },
            "required": [
                "fastq",
                "ref_genome"
            ]
        },
        "meta_data": {
            "title": "Meta Data",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "report_name": {
                    "type": "string",
                    "default": "report",
                    "description": "Output report filename suffix."
                }
            }
        },
        "generic_options": {
            "title": "Generic options",
            "type": "object",
            "fa_icon": "far fa-question-circle",
            "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
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/basic_input_output_options"
        },
        {
            "$ref": "#/definitions/meta_data"
        },
        {
            "$ref": "#/definitions/generic_options"
        }
    ],
    "properties": {
        "aws_image_prefix": {
            "type": "string",
            "hidden": true
        },
        "aws_queue": {
            "type": "string",
            "hidden": true
        },
        "wfversion": {
            "type": "string",
            "default": "v0.3.3",
            "hidden": true
        },
        "monochrome_logs": {
            "type": "boolean"
        },
        "validate_params": {
            "type": "boolean",
            "default": true
        },
        "show_hidden_params": {
            "type": "boolean"
        }
    }
}