treeval/assets/schema_input.json at a5fe0d8944e872491bf992bdaf6491bc99f6d297 · sanger-tol/treeval · GitHub

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{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/sanger-tol/treeval/master/assets/schema_input.json",
    "title": "sanger-tol/treeval pipeline - params.input schema",
    "description": "Schema for the file provided with params.input",
    "type": "object",
    "properties": {
        "assembly": {
            "type": "object",
            "properties": {
                "assem_level": {
                    "type": "string",
                    "errorMessage": "Assembly level must be provided"
                },
                "assem_version": {
                    "anyOf": [
                        {
                            "type": "string"
                        },
                        {
                            "type": "integer"
                        }
                    ],
                    "errorMessage": "Assembly version must be provided"
                },
                "sample_id": {
                    "type": "string",
                    "errorMessage": "Sample name must be provided and cannot contain spaces"
                },
                "latin_name": {
                    "type": "string",
                    "errorMessage": "The scientific name for the assembly"
                },
                "defined_class": {
                    "type": "string",
                    "errorMessage": "The Clade of the assembly. Used as the syntenic group and to complete the gene_alignment data dir."
                },
                "project_id": {
                    "type": "string",
                    "errorMessage": "Project name must be provided "
                }
            }
        },
        "reference_file": {
            "type": "string",
            "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
            "errorMessage": "Assembly input file"
        },
        "map_order": {
            "type": "string",
            "errorMessage": "Map order",
            "enum": [
                "length",
                "unsorted"
            ]
        },
        "assem_reads": {
            "type": "object",
            "properties": {
                "read_type": {
                    "type": "string",
                    "errorMessage": "Long read data type",
                    "enum": [
                        "hifi",
                        "clr",
                        "ont",
                        "illumina"
                    ]
                },
                "read_data": {
                    "type": "array",
                    "errorMessage": "Paths to fasta.gz files and/or FOFN of fasta.gz files",
                    "pattern": "(^\\S+\\.(fa|fasta|fna).gz)$|(^\\S+\\.fofn)$",
                    "format": "file-path",
                    "exists": true
                },
                "supplementary_data": {
                    "type": "string",
                    "errorMessage": "Not currently in use. Placeholder for future use"
                }
            }
        },
        "hic_data": {
            "type": "object",
            "properties": {
                "hic_cram": {
                    "type": "array",
                    "errorMessage": "Paths to an array of cram files and/or FOFN of cram files",
                    "pattern": "(^\\S+\\.cram)$|(^\\S+\\.fofn)$",
                    "format": "file-path",
                    "exists": true
                },
                "hic_aligner": {
                    "type": "string",
                    "errorMessage": "HiC Aligner - minimap2 (default), bwamem2",
                    "enum": [
                        "minimap2",
                        "bwamem2"
                    ]
                }
            }
        },
        "kmer_profile": {
            "type": "object",
            "properties": {
                "kmer_length": {
                    "type": "integer",
                    "errorMessage": "K-mer length"
                },
                "profile": {
                    "type": "string",
                    "errorMessage": "Path to *.hist file"
                }
            }
        },
        "alignment": {
            "type": "object",
            "properties": {
                "genesets": {
                    "type": "array",
                    "errorMessage": "Path for gene alignment file.",
                    "pattern": "^\\S+\\.csv$"
                }
            }
        },
        "self_comp": {
            "type": "object",
            "properties": {
                "motif_len": {
                    "type": "integer",
                    "errorMessage": "Length of motif to be used in self comp search"
                }
            }
        },
        "intron": {
            "type": "object",
            "properties": {
                "size": {
                    "type": "string",
                    "errorMessage": "Base pair size of introns, defaults to 50k"
                }
            }
        },
        "telomere": {
            "type": "object",
            "properties": {
                "teloseq": {
                    "type": "string",
                    "errorMessage": "Expected telomeric motif"
                }
            }
        },
        "synteny": {
            "type": "array",
            "pattern": "^\\S+\\.(fa|fasta|fna)$"
        },
        "busco": {
            "type": "object",
            "properties": {
                "lineage_path": {
                    "type": "string",
                    "errorMessage": "Path to directory containing lineages folder"
                },
                "lineage": {
                    "type": "string",
                    "errorMessage": "busco lineage to run"
                }
            }
        }
    },
    "required": [
        "busco",
        "synteny",
        "telomere",
        "intron",
        "self_comp",
        "alignment",
        "kmer_profile",
        "hic_data",
        "assem_reads",
        "map_order",
        "reference_file",
        "assembly"
    ]
}