eager/assets/schema_input.json at dd81b54f4f650832b79c9b2d6d2ef4639b7a09e4 · aidaanva/eager · GitHub

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{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/eager/master/assets/schema_input.json",
    "title": "nf-core/eager pipeline - params.input schema",
    "description": "Schema for the file provided with params.input",
    "type": "array",
    "items": {
        "type": "object",
        "properties": {
            "sample_id": {
                "type": "string",
                "pattern": "^\\S+$",
                "meta": ["sample_id"],
                "errorMessage": "Sample name must be provided and cannot contain spaces."
            },
            "library_id": {
                "type": "string",
                "pattern": "^\\S+$",
                "meta": ["library_id"],
                "errorMessage": "Library name must be provided and cannot contain spaces."
            },
            "lane": {
                "type": "integer",
                "meta": ["lane"],
                "errorMessage": "Sequencing lane number must be provided and specified as an integer. If no lane information, specify 0."
            },
            "colour_chemistry": {
                "type": "integer",
                "enum": [2, 4],
                "meta": ["colour_chemistry"],
                "errorMessage": "Sequencing colour chemistry must be provided and specified as '2' for Illumina NextSeq/NovaSeq or '4' Illumina MiSeq/HiSeq/BGI."
            },
            "pairment": {
                "type": "string",
                "enum": ["single", "paired"],
                "meta": ["pairment"],
                "errorMessage": "Sequencing pairment must be provided and specified as 'single' or 'paired'. BAM files containing merged reads should be specified as 'single'."
            },
            "strandedness": {
                "type": "string",
                "enum": ["single", "double"],
                "meta": ["strandedness"],
                "errorMessage": "Library strandedness must be provided and specified as 'single' or 'double'."
            },
            "damage_treatment": {
                "type": "string",
                "enum": ["none", "half", "full"],
                "meta": ["damage_treatment"],
                "errorMessage": "Library damage treatment must be provided and specified as 'none', 'half' or 'full'."
            },
            "r1": {
                "type": "string",
                "format": "file-path",
                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
                "exists": true,
                "errorMessage": "FastQ file for read 1 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'."
            },
            "r2": {
                "type": "string",
                "format": "file-path",
                "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$",
                "exists": true,
                "errorMessage": "FastQ file for read 2 require sister file for read 1, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'."
            },
            "bam": {
                "type": "string",
                "format": "file-path",
                "pattern": "^\\S+\\.bam$",
                "exists": true,
                "errorMessage": "BAM files cannot contain any spaces and must have extension '.bam'."
            },
            "bam_reference_id": {
                "type": "string",
                "meta": ["bam_reference_id"],
                "errorMessage": "A BAM reference ID (corresponding to what is supplied to `--fasta`) must always be provided when providing a BAM file."
            },
            "vcf": {
                "type": "string",
                "format": "file-path",
                "pattern": "^\\S+\\.vcf.gz$",
                "exists": true,
                "errorMessage": "VCFs files cannot contain any spaces and must have extension '.vcf.gz' and be gzip zipped."
            },
            "vcf_reference_id": {
                "type": "string",
                "meta": ["vcf_reference_id"],
                "errorMessage": "A VCF reference ID (corresponding to what is supplied to `--fasta`) must always be provided when providing a VCF file."
            }
        },
        "required": [
            "sample_id",
            "library_id",
            "lane",
            "colour_chemistry",
            "pairment",
            "strandedness",
            "damage_treatment"
        ],
        "anyOf": [
            {
                "required": ["r1"]
            },
            {
                "required": ["bam"]
            },
            {
                "required": ["vcf"]
            }
        ],
        "dependentRequired": {
            "r2": ["r1"],
            "bam": ["bam_reference_id"],
            "bam_reference_id": ["bam"],
            "vcf" : ["vcf_reference_id"],
            "vcf_reference_id" : ["vcf"]
        }
    },
    "allOf": [
        { "uniqueEntries": ["lane", "library_id"] },
        { "uniqueEntries": "r1" },
        { "uniqueEntries": "r2" },
        { "uniqueEntries": "bam" },
        { "uniqueEntries": "vcf" }
    ]
}