<commit_before>{
    "title": "Reference file",
    "description": "Files used in pipelines as references.",
    "id": "/profiles/file_reference.json",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "required": ["file_format", "award", "lab"],
    "identifyingProperties": ["uuid", "accession", "aliases"],
    "additionalProperties": false,
    "mixinProperties": [
        { "$ref": "mixins.json#/schema_version" },
        { "$ref": "mixins.json#/uuid" },
        { "$ref": "mixins.json#/submitted" },
        { "$ref": "mixins.json#/modified" },
        { "$ref": "mixins.json#/release_dates" },
        { "$ref": "mixins.json#/aliases" },
        { "$ref": "mixins.json#/attribution" },
        { "$ref": "mixins.json#/notes" },
        { "$ref": "mixins.json#/accession" },
        { "$ref": "mixins.json#/dbxrefs" },
        { "$ref": "mixins.json#/tags" },
        { "$ref": "file.json#/properties" }
    ],
    "mixinFacets": [
        { "$ref": "file.json#/facets"},
        { "$ref": "mixins.json#/facets_common" }
    ],
    "mixinColumns": [
        { "$ref": "file.json#/columns"}
    ],
    "properties": {
        "schema_version": {
            "default": "1"
        },
        "file_format": {
            "title": "File Format",
            "type": "string",
            "enum": [
                "bwaIndex",
                "chromsizes",
                "reference_fasta",
                "oligo_fasta",
                "juicer_format_restriction_site_file",
                "other"
            ]
        },
        "file_type": {
            "title": "File Type",
            "description": "The type of file based on the information in the file.",
            "enum": [
                "genome reference",
                "genome index",
                "index",
                "oligo sequences",
                "restriction sites",
                "blacklisted regions",
                "repeats",
                "other"
            ]
        },
        "file_classification": {
            "title": "General Classification",
            "type": "string",
            "default": "ancillary file",
            "exclude_from": ["submit4dn", "FFedit-create"],
            "enum": [
                "ancillary file"
            ]
        }
    },
    "file_format_file_extension": {
        "bwaIndex": ".bwaIndex.tgz",
        "chromsizes": ".chrom.sizes",
        "reference_fasta": ".fasta.gz",
        "oligo_fasta": ".fasta",
        "juicer_format_restriction_site_file": ".txt",
        "other": ""
    }
}<commit_msg>Changed file formats in file_reference.json - reference_fasta changed to compressed_fasta, oligo_fasta changed to fasta to make them more widely applicable<commit_after>{
    "title": "Reference file",
    "description": "Files used in pipelines as references.",
    "id": "/profiles/file_reference.json",
    "$schema": "http://json-schema.org/draft-04/schema#",
    "type": "object",
    "required": ["file_format", "award", "lab"],
    "identifyingProperties": ["uuid", "accession", "aliases"],
    "additionalProperties": false,
    "mixinProperties": [
        { "$ref": "mixins.json#/schema_version" },
        { "$ref": "mixins.json#/uuid" },
        { "$ref": "mixins.json#/submitted" },
        { "$ref": "mixins.json#/modified" },
        { "$ref": "mixins.json#/release_dates" },
        { "$ref": "mixins.json#/aliases" },
        { "$ref": "mixins.json#/attribution" },
        { "$ref": "mixins.json#/notes" },
        { "$ref": "mixins.json#/accession" },
        { "$ref": "mixins.json#/dbxrefs" },
        { "$ref": "mixins.json#/tags" },
        { "$ref": "file.json#/properties" }
    ],
    "mixinFacets": [
        { "$ref": "file.json#/facets"},
        { "$ref": "mixins.json#/facets_common" }
    ],
    "mixinColumns": [
        { "$ref": "file.json#/columns"}
    ],
    "properties": {
        "schema_version": {
            "default": "1"
        },
        "file_format": {
            "title": "File Format",
            "type": "string",
            "enum": [
                "bwaIndex",
                "chromsizes",
                "compressed_fasta",
                "fasta",
                "juicer_format_restriction_site_file",
                "other"
            ]
        },
        "file_type": {
            "title": "File Type",
            "description": "The type of file based on the information in the file.",
            "enum": [
                "genome reference",
                "genome index",
                "index",
                "oligo sequences",
                "restriction sites",
                "blacklisted regions",
                "repeats",
                "other"
            ]
        },
        "file_classification": {
            "title": "General Classification",
            "type": "string",
            "default": "ancillary file",
            "exclude_from": ["submit4dn", "FFedit-create"],
            "enum": [
                "ancillary file"
            ]
        }
    },
    "file_format_file_extension": {
        "bwaIndex": ".bwaIndex.tgz",
        "chromsizes": ".chrom.sizes",
        "compressed_fasta": ".fasta.gz",
        "fasta": ".fasta",
        "juicer_format_restriction_site_file": ".txt",
        "other": ""
    }
}
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