blobtoolkit/assets/schema_input.json at c74dcea9c94c6cffc70eaaeb1697e07242824ca3 · sanger-tol/blobtoolkit · GitHub

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{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/sanger-tol/blobtoolkit/main/assets/schema_input.json",
    "title": "sanger-tol/blobtoolkit pipeline - params.input schema",
    "description": "Schema for the file provided with params.input",
    "type": "array",
    "items": {
        "type": "object",
        "properties": {
            "sample": {
                "type": "string",
                "description": "Sample identifier",
                "pattern": "^\\S+$",
                "errorMessage": "Sample name must be provided, be unique, and cannot contain spaces",
                "meta": ["id"]
            },
            "datatype": {
                "type": "string",
                "pattern": "^\\S+$",
                "enum": ["hic", "illumina", "ont", "pacbio", "pacbio_clr"],
                "errorMessage": "Data type must be one of: 'hic' or 'illumina' or 'ont' or 'pacbio'",
                "meta": ["datatype"]
            },
            "datafile": {
                "type": "string",
                "format": "file-path",
                "exists": true,
                "pattern": "^\\S+\\.(bam|cram|fa|fa.gz|fasta|fasta.gz|fq|fq.gz|fastq|fastq.gz)$",
                "errorMessage": "Data file for reads cannot contain spaces and must be BAM/CRAM/FASTQ/FASTA"
            },
            "library_layout": {
                "type": "string",
                "pattern": "^(SINGLE|PAIRED)$",
                "errorMessage": "The only valid layouts are SINGLE and PAIRED",
                "meta": ["layout"]
            }
        },
        "required": ["datafile", "datatype", "sample"]
    },
    "uniqueEntries": ["sample"]
}