396 lines
15 KiB
YAML
396 lines
15 KiB
YAML
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definitions:
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Config:
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description: "A Viash configuration is a YAML file which contains metadata to\
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\ describe the behaviour and build target(s) of a component. \nWe commonly\
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\ name this file `config.vsh.yaml` in our examples, but you can name it however\
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\ you choose. \n"
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type: "object"
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properties:
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label:
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description: "A clean version of the component's name. This is only used for\
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\ documentation."
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type: "string"
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license:
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description: "The license of the package."
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type: "string"
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authors:
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description: "A list of authors. An author must at least have a name, but\
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\ can also have a list of roles, an e-mail address, and a map of custom\
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\ properties.\n\nSuggested values for roles are:\n \n| Role | Abbrev. |\
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\ Description |\n|------|---------|-------------|\n| maintainer | mnt |\
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\ for the maintainer of the code. Ideally, exactly one maintainer is specified.\
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\ |\n| author | aut | for persons who have made substantial contributions\
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\ to the software. |\n| contributor | ctb| for persons who have made smaller\
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\ contributions (such as code patches).\n| datacontributor | dtc | for persons\
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\ or organisations that contributed data sets for the software\n| copyrightholder\
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\ | cph | for all copyright holders. This is a legal concept so should use\
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\ the legal name of an institution or corporate body.\n| funder | fnd |\
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\ for persons or organizations that furnished financial support for the\
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\ development of the software\n\nThe [full list of roles](https://www.loc.gov/marc/relators/relaterm.html)\
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\ is extremely comprehensive.\n"
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type: "array"
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items:
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type: object
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properties:
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__merge__:
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type: string
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pattern: "^/src/authors/.*\\.yaml$"
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roles:
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description: |
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Role of the author. Possible values:
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* `"author"`: Authors who have made substantial contributions to the component.
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* `"maintainer"`: The maintainer of the component.
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* `"contributor"`: Authors who have made smaller contributions (such as code patches etc.).
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type: array
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items:
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enum: [maintainer, author, contributor]
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status:
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description: "Allows setting a component to active, deprecated or disabled."
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$ref: "defs_viash.yaml#/definitions/Status"
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requirements:
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description: "Computational requirements related to running the component.\
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\ \n`cpus` specifies the maximum number of (logical) cpus a component is\
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\ allowed to use., whereas\n`memory` specifies the maximum amount of memory\
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\ a component is allowed to allicate. Memory units must be\nin B, KB, MB,\
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\ GB, TB or PB for SI units (1000-base), or KiB, MiB, GiB, TiB or PiB for\
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\ binary IEC units (1024-base)."
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$ref: "defs_viash.yaml#/definitions/ComputationalRequirements"
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repositories:
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description: "(Pre-)defines repositories that can be used as repository in\
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\ dependencies.\nAllows reusing repository definitions in case it is used\
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\ in multiple dependencies."
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type: "array"
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items:
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$ref: "defs_viash.yaml#/definitions/RepositoryWithName"
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dependencies:
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description: "Allows listing Viash components required by this Viash component"
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type: "array"
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items:
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$ref: "defs_viash.yaml#/definitions/Dependency"
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summary:
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description: "A one-sentence summary of the component. This is only used for\
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\ documentation."
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type: "string"
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runners:
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description: "A list of runners to execute target artifacts.\n\n - ExecutableRunner\n\
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\ - NextflowRunner\n"
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type: "array"
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items:
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$ref: "defs_viash.yaml#/definitions/Runner"
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name:
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description: "Name of the component and the filename of the executable when\
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\ built with `viash build`."
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type: "string"
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argument_groups:
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description: "A grouping of the arguments, used to display the help message.\n\
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\n - `name: foo`, the name of the argument group. \n - `description: Description\
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\ of foo`, a description of the argument group. Multiline descriptions are\
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\ supported.\n - `arguments: [arg1, arg2, ...]`, list of the arguments.\n\
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\n"
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type: "array"
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items:
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$ref: "defs_viash.yaml#/definitions/ArgumentGroup"
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description:
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description: "A description of the component. This is only used for documentation.\
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\ Multiline descriptions are supported."
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type: "string"
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usage:
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description: "A description on how to use the component. This will be displayed\
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\ with `--help` under the 'Usage:' section."
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type: "string"
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info:
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description: "Structured information. Can be any shape: a string, vector,\
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\ map or even nested map."
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type: "object"
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version:
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description: "Version of the component. This field will be used to version\
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\ the executable and the Docker container."
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type: "string"
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links:
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description: "External links of the component."
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$ref: "defs_viash.yaml#/definitions/Links"
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references:
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description: "References to external resources related to the component."
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$ref: "defs_viash.yaml#/definitions/References"
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engines:
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description: "A list of engine environments to execute target artifacts in.\n\
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\n - NativeEngine\n - DockerEngine\n"
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type: "array"
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items:
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$ref: "defs_viash.yaml#/definitions/Engine"
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resources:
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description: "Resources are files that support the component. The first resource\
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\ should be a script that will be executed when the component is run. Additional\
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\ resources will be copied to the same directory.\n\nCommon properties:\n\
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\n * type: `file` / `r_script` / `python_script` / `bash_script` / `javascript_script`\
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\ / `scala_script` / `csharp_script`, specifies the type of the resource.\
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\ The first resource cannot be of type `file`. When the type is not specified,\
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\ the default type is simply `file`.\n * dest: filename, the resulting name\
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\ of the resource. From within a script, the file can be accessed at `meta[\"\
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resources_dir\"] + \"/\" + dest`. If unspecified, `dest` will be set to\
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\ the basename of the `path` parameter.\n * path: `path/to/file`, the path\
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\ of the input file. Can be a relative or an absolute path, or a URI. Mutually\
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\ exclusive with `text`.\n * text: ...multiline text..., the content of\
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\ the resulting file specified as a string. Mutually exclusive with `path`.\n\
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\ * is_executable: `true` / `false`, whether the resulting resource file\
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\ should be made executable.\n"
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type: "array"
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items:
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$ref: "defs_viash.yaml#/definitions/Resource"
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keywords:
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description: "The keywords of the components."
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type: "array"
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items:
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type: "string"
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test_resources:
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description: "One or more scripts to be used to test the component behaviour\
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\ when `viash test` is invoked. Additional files of type `file` will be\
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\ made available only during testing. Each test script should expect no\
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\ command-line inputs, be platform-independent, and return an exit code\
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\ >0 when unexpected behaviour occurs during testing. See Unit Testing for\
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\ more info."
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type: "array"
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items:
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$ref: "defs_viash.yaml#/definitions/Resource"
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namespace:
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description: "Namespace this component is a part of. See the Namespaces guide\
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\ for more information on namespaces."
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type: "string"
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arguments:
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description: "A list of arguments for this component. For each argument, a\
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\ type and a name must be specified. Depending on the type of argument,\
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\ different properties can be set. See these reference pages per type for\
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\ more information: \n\n - string\n - file\n - integer\n - double\n - boolean\n\
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\ - boolean_true\n - boolean_false\n"
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type: "array"
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items:
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$ref: "defs_viash.yaml#/definitions/Argument"
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__merge__:
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$ref: "#/definitions/Merge"
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required:
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- "name"
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additionalProperties: false
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Merge:
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type: string
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description: Path to a YAML file to inherit values from.
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oneOf:
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- type: array
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- type: string
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FileFormat:
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description: 'File format metadata'
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type: object
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required: [label, file_format]
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properties:
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label:
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$ref: "defs_common.yaml#/definitions/Label"
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summary:
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$ref: "defs_common.yaml#/definitions/Summary"
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file_format:
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oneOf:
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- type: object
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required: [type]
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additionalProperties: false
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properties:
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type:
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const: h5ad
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X:
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$ref: "#/definitions/AnnDataSlot"
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layers:
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type: array
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items:
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$ref: "#/definitions/AnnDataSlot"
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var:
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type: array
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items:
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$ref: "#/definitions/AnnDataSlot"
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varm:
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type: array
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items:
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$ref: "#/definitions/AnnDataSlot"
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varp:
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type: array
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items:
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$ref: "#/definitions/AnnDataSlot"
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obs:
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type: array
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items:
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$ref: "#/definitions/AnnDataSlot"
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obsm:
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type: array
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items:
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$ref: "#/definitions/AnnDataSlot"
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obsp:
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type: array
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items:
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$ref: "#/definitions/AnnDataSlot"
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uns:
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type: array
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items:
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oneOf:
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- $ref: "#/definitions/AnnDataSlot"
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- $ref: "#/definitions/AnnDataSlotObject"
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- type: object
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required: [type, mod]
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additionalProperties: false
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properties:
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type:
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const: h5mu
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mod:
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type: object
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additionalProperties: false
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properties:
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rna:
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"#/definitions/AnnData"
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atac:
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"#/definitions/AnnData"
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prot:
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"#/definitions/AnnData"
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vdj:
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"#/definitions/AnnData"
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vdj_t:
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"#/definitions/AnnData"
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vdj_b:
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"#/definitions/AnnData"
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gdo:
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"#/definitions/AnnData"
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hto:
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"#/definitions/AnnData"
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MuData:
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required: [mod]
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additionalProperties: false
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properties:
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mod:
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type: object
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additionalProperties: false
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properties:
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rna:
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"#/definitions/AnnData"
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atac:
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"#/definitions/AnnData"
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prot:
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"#/definitions/AnnData"
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vdj:
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"#/definitions/AnnData"
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vdj_t:
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"#/definitions/AnnData"
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vdj_b:
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"#/definitions/AnnData"
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gdo:
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"#/definitions/AnnData"
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hto:
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"#/definitions/AnnData"
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AnnData:
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additionalProperties: false
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properties:
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X:
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$ref: "#/definitions/AnnDataSlot"
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layers:
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type: array
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items:
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$ref: "#/definitions/AnnDataSlot"
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var:
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type: array
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items:
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$ref: "#/definitions/AnnDataSlot"
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varm:
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type: array
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items:
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$ref: "#/definitions/AnnDataSlot"
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varp:
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type: array
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items:
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$ref: "#/definitions/AnnDataSlot"
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obs:
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type: array
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items:
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$ref: "#/definitions/AnnDataSlot"
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obsm:
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type: array
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items:
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$ref: "#/definitions/AnnDataSlot"
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obsp:
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type: array
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items:
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$ref: "#/definitions/AnnDataSlot"
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uns:
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type: array
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items:
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oneOf:
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- $ref: "#/definitions/AnnDataSlot"
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- $ref: "#/definitions/AnnDataSlotObject"
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AnnDataSlot:
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properties:
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type:
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enum: [integer, double, string, boolean]
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name:
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type: string
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description: A unique identifier.
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pattern: "^[a-zA-Z_][a-zA-Z0-9_]*$"
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|
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description:
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type: string
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required:
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type: boolean
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required: [type, name, description, required]
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AnnDataSlotObject:
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properties:
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||
|
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type:
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enum: [object]
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name:
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type: string
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description: A unique identifier.
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pattern: "^[a-zA-Z_][a-zA-Z0-9_]*$"
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|
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description:
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type: string
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required:
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type: boolean
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required: [type, name, description, required]
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|
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# added specific properties to the author info
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Author:
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description: Author metadata.
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type: object
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||
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additionalProperties: false
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properties:
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name:
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description: Full name of the author, usually in the name of FirstName MiddleName LastName.
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type: string
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info:
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description: Additional information on the author
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type: object
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additionalProperties: false
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required: [role, links, organizations]
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properties:
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links:
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||
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type: object
|
||
|
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additionalProperties: false
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||
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required: github
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||
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properties:
|
||
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github:
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||
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type: string
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orcid:
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type: string
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email:
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type: string
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twitter:
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||
|
|
type: string
|
||
|
|
linkedin:
|
||
|
|
type: string
|
||
|
|
role:
|
||
|
|
description: Role in the organisation
|
||
|
|
enum: ["Core Team Member", "Contributor"]
|
||
|
|
organizations:
|
||
|
|
type: array
|
||
|
|
minItems: 1
|
||
|
|
items:
|
||
|
|
type: object
|
||
|
|
additionalProperties: false
|
||
|
|
required: [name, href, role]
|
||
|
|
properties:
|
||
|
|
name:
|
||
|
|
type: string
|
||
|
|
href:
|
||
|
|
type: string
|
||
|
|
role:
|
||
|
|
type: string
|