nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/grp-bork/samestr_flow/main/nextflow_schema.json",
    "title": "samestr_flow pipeline parameters",
    "description": "samestr_flow JSON schema",
    "type": "object",
    "definitions": {    
        "preprocessing": {
            "title": "preprocessing",
            "type": "object",
            "description": "Preprocessing parameters",
            "default": "",
            "properties": {
                "qc_minlen": {
                    "type": "integer",
                    "description": "Minimum read length to pass quality control",
                    "default": 45
                },
                "qc_params_shotgun": {
                    "type": "string",
                    "description": "bbduk quality control parameters",
                    "default": "qtrim=rl trimq=25 maq=25 ktrim=r k=23 mink=11 hdist=1 ftm=5 entropy=0.5 entropywindow=50 entropyk=5 tpe tbo"
                },
                "remove_host_kraken2_db": {
                    "type": "string",
					"format": "directory-path",
					"hidden": true,
                    "description": "Path to a kraken2 database",
					"default": "/vol/data/databases/clowm/CLDB-018fde8b0aa373a5ba7d3236bb921cc9/018fde8b0aac74889c57f7b1af5f87cb/hg38_silva_genome"
                }
            },
            "required": [
                "qc_minlen",
                "qc_params_shotgun",
                "remove_host_kraken2_db"
            ]
        },
        "required": {
            "title": "Required",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "input_dir": {
                    "type": "string",
                    "description": "Directory path to fastq files",
                    "format": "directory-path"
                },
                "output_dir": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Path to output directory"
                },
                "mp4_db": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Path to metaphlan4 database",
					"hidden": true,
                    "default": "/vol/data/databases/clowm/CLDB-0190034231947aec9710260cbaea023c/01900c514077794fa92645bc6a3ee4db"
                },
				"samestr_marker_db": {
                    "type": "string",
                    "format": "directory-path",
                    "description": "Path to samestr marker database",
					"hidden": true,
                    "default": "/vol/data/databases/clowm/CLDB-0190035a020874b2b26a678a86dd3bd0/0190035a021079518f9579a8a1db7f05/SameStr_mpa_vJun23_CHOCOPhlAnSGB_202307"
                }
			},
            "required": [
                "input_dir",
                "output_dir",
				"mp4_db",
				"samestr_marker_db"
            ]
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/preprocessing"
        },
        {
            "$ref": "#/definitions/required"
        }
    ],
    "properties": {
        "run_preprocessing": {
            "type": "boolean",
            "default": true
        },
        "remove_host": {
            "type": "boolean",
            "default": true
        },
        "drop_orphans": {
            "type": "boolean",
            "hidden": true,
            "default": true
        },
        "kraken2_min_hit_groups": {
            "type": "integer",
            "hidden": true,
            "default": 10
        }
    }
}