funcscan/assets/schema_input.json at 97c9bb90141a4e3c8b0029bf1aa9572ac5ad8593 · HaidYi/funcscan · GitHub

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{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/funcscan/master/assets/schema_input.json",
    "title": "nf-core/funcscan pipeline - params.input schema",
    "description": "Schema for the file provided with params.input",
    "type": "array",
    "items": {
        "type": "object",
        "properties": {
            "sample": {
                "type": "string",
                "pattern": "^\\S+$",
                "errorMessage": "Sample ID must be provided, must be an integer or string and cannot contain spaces",
                "meta": ["id"]
            },
            "fasta": {
                "type": "string",
                "format": "file-path",
                "exists": true,
                "pattern": "^\\S+\\.(fasta|fas|fna|fa)(\\.gz)?$",
                "errorMessage": "Fasta file for reads must be provided, cannot contain spaces and must have extension `.fa`, `.fa.gz`, `.fna`, `.fna.gz`, `.fasta`, or `.fasta.gz`"
            },
            "protein": {
                "type": "string",
                "format": "file-path",
                "exists": true,
                "pattern": "^\\S+\\.(faa|fasta)(\\.gz)?$",
                "errorMessage": "Input file for peptide annotations has incorrect file format. File must end in `.fasta`, `.fasta.gz`, `.faa`, or `.faa.gz`"
            },
            "gbk": {
                "type": "string",
                "format": "file-path",
                "exists": true,
                "pattern": "^\\S+\\.(gbk|gbff)(\\.gz)?$",
                "errorMessage": "Input file for feature annotations has incorrect file format. File must end in `.gbk`, `.gbk.gz` or `.gbff`, or `.gbff.gz`"
            },
            "gff": {
                "type": "string",
                "format": "file-path",
                "exists": true,
                "pattern": "^\\S+\\.(gff|gff3)(\\.gz)?$",
                "errorMessage": "Input file for feature annotations has incorrect file format. File must end in `.gff`, `.gff.gz` or `.gff3`, or `.gff3.gz`"
            },
            "gff_type": {
                "type": "string",
                "enum": ["NCBI_prok", "prodigal", "NCBI_euk", "JGI"],
                "errorMessage": "GFF type must be one of: NCBI_prok, prodigal, NCBI_euk, or JGI",
                "meta": ["gff_type"]
            }
        },
        "required": ["sample", "fasta"],
        "dependentRequired": {
            "protein": ["gbk"],
            "gbk": ["protein"],
            "gff": ["protein"]
        }
    },
    "uniqueItems": true
}