{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/bactopia/bactopia/master/modules/nf-core/ismapper/params.json",
    "title": "ISMapper Module",
    "description": "A module for identifying insertion sites",
    "type": "object",
    "definitions": {
        "ismapper_parameters": {
            "title": "ISMapper Parameters",
            "type": "object",
            "description": "",
            "default": "",
            "fa_icon": "fas fa-exclamation-circle",
            "properties": {
                "reference": {
                    "type": "string",
                    "description": "Reference genome for typing against in GenBank format",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "is_required": true
                },
                "insertions": {
                    "type": "string",
                    "description": "Multifasta file with insertion sequence(s) to be mapped to",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "is_required": true
                },
                "min_clip": {
                    "type": "integer",
                    "default": 10,
                    "description": "Minimum size for softclipped region to be extracted from initial mapping",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "max_clip": {
                    "type": "integer",
                    "default": 30,
                    "description": "Maximum size for softclipped regions to be included",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "cutoff": {
                    "type": "integer",
                    "default": 6,
                    "description": "Minimum depth for mapped region to be kept in bed file",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "novel_gap_size": {
                    "type": "integer",
                    "default": 15,
                    "description": "Distance in base pairs between left and right flanks to be called a novel hit",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "min_range": {
                    "type": "number",
                    "default": 0.9,
                    "description": "Minimum percent size of the gap to be called a known hit",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "max_range": {
                    "type": "number",
                    "default": 1.1,
                    "description": "Maximum percent size of the gap to be called a known hit",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "merging": {
                    "type": "integer",
                    "default": 100,
                    "description": "Value for merging left and right hits in bed files together to simply calculation of closest and intersecting regions",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "ismap_all": {
                    "type": "boolean",
                    "default": false,
                    "description": "Switch on all alignment reporting for bwa",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                },
                "ismap_minqual": {
                    "type": "integer",
                    "default": 30,
                    "description": "Mapping quality score for bwa",
                    "fa_icon": "fas fa-expand-arrows-alt",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/ismapper_parameters"
        }
    ]
}
