definitions:
  Config:
    description: "A Viash configuration is a YAML file which contains metadata to\
      \ describe the behaviour and build target(s) of a component.  \nWe commonly\
      \ name this file `config.vsh.yaml` in our examples, but you can name it however\
      \ you choose.  \n"
    type: "object"
    properties:
      label:
        description: "A clean version of the component's name. This is only used for\
          \ documentation."
        type: "string"
      license:
        description: "The license of the package."
        type: "string"
      authors:
        description: "A list of authors. An author must at least have a name, but\
          \ can also have a list of roles, an e-mail address, and a map of custom\
          \ properties.\n\nSuggested values for roles are:\n \n| Role | Abbrev. |\
          \ Description |\n|------|---------|-------------|\n| maintainer | mnt |\
          \ for the maintainer of the code. Ideally, exactly one maintainer is specified.\
          \ |\n| author | aut | for persons who have made substantial contributions\
          \ to the software. |\n| contributor | ctb| for persons who have made smaller\
          \ contributions (such as code patches).\n| datacontributor | dtc | for persons\
          \ or organisations that contributed data sets for the software\n| copyrightholder\
          \ | cph | for all copyright holders. This is a legal concept so should use\
          \ the legal name of an institution or corporate body.\n| funder | fnd |\
          \ for persons or organizations that furnished financial support for the\
          \ development of the software\n\nThe [full list of roles](https://www.loc.gov/marc/relators/relaterm.html)\
          \ is extremely comprehensive.\n"
        type: "array"
        items:
          type: object
          properties:
            __merge__:
              type: string
              pattern: "^/src/authors/.*\\.yaml$"
            roles:
              description: |
                  Role of the author. Possible values:

                  * `"author"`: Authors who have made substantial contributions to the component.
                  * `"maintainer"`: The maintainer of the component.
                  * `"contributor"`: Authors who have made smaller contributions (such as code patches etc.).
              type: array
              items:
                enum: [maintainer, author, contributor]
      status:
        description: "Allows setting a component to active, deprecated or disabled."
        $ref: "defs_viash.yaml#/definitions/Status"
      requirements:
        description: "Computational requirements related to running the component.\
          \ \n`cpus` specifies the maximum number of (logical) cpus a component is\
          \ allowed to use., whereas\n`memory` specifies the maximum amount of memory\
          \ a component is allowed to allicate. Memory units must be\nin B, KB, MB,\
          \ GB, TB or PB for SI units (1000-base), or KiB, MiB, GiB, TiB or PiB for\
          \ binary IEC units (1024-base)."
        $ref: "defs_viash.yaml#/definitions/ComputationalRequirements"
      repositories:
        description: "(Pre-)defines repositories that can be used as repository in\
          \ dependencies.\nAllows reusing repository definitions in case it is used\
          \ in multiple dependencies."
        type: "array"
        items:
          $ref: "defs_viash.yaml#/definitions/RepositoryWithName"
      dependencies:
        description: "Allows listing Viash components required by this Viash component"
        type: "array"
        items:
          $ref: "defs_viash.yaml#/definitions/Dependency"
      summary:
        description: "A one-sentence summary of the component. This is only used for\
          \ documentation."
        type: "string"
      runners:
        description: "A list of runners to execute target artifacts.\n\n - ExecutableRunner\n\
          \ - NextflowRunner\n"
        type: "array"
        items:
          $ref: "defs_viash.yaml#/definitions/Runner"
      name:
        description: "Name of the component and the filename of the executable when\
          \ built with `viash build`."
        type: "string"
      argument_groups:
        description: "A grouping of the arguments, used to display the help message.\n\
          \n - `name: foo`, the name of the argument group. \n - `description: Description\
          \ of foo`, a description of the argument group. Multiline descriptions are\
          \ supported.\n - `arguments: [arg1, arg2, ...]`, list of the arguments.\n\
          \n"
        type: "array"
        items:
          $ref: "defs_viash.yaml#/definitions/ArgumentGroup"
      description:
        description: "A description of the component. This is only used for documentation.\
          \ Multiline descriptions are supported."
        type: "string"
      usage:
        description: "A description on how to use the component. This will be displayed\
          \ with `--help` under the 'Usage:' section."
        type: "string"
      info:
        description: "Structured information. Can be any shape: a string, vector,\
          \ map or even nested map."
        type: "object"
      version:
        description: "Version of the component. This field will be used to version\
          \ the executable and the Docker container."
        type: "string"
      links:
        description: "External links of the component."
        $ref: "defs_viash.yaml#/definitions/Links"
      references:
        description: "References to external resources related to the component."
        $ref: "defs_viash.yaml#/definitions/References"
      engines:
        description: "A list of engine environments to execute target artifacts in.\n\
          \n - NativeEngine\n - DockerEngine\n"
        type: "array"
        items:
          $ref: "defs_viash.yaml#/definitions/Engine"
      resources:
        description: "Resources are files that support the component. The first resource\
          \ should be a script that will be executed when the component is run. Additional\
          \ resources will be copied to the same directory.\n\nCommon properties:\n\
          \n * type: `file` / `r_script` / `python_script` / `bash_script` / `javascript_script`\
          \ / `scala_script` / `csharp_script`, specifies the type of the resource.\
          \ The first resource cannot be of type `file`. When the type is not specified,\
          \ the default type is simply `file`.\n * dest: filename, the resulting name\
          \ of the resource.  From within a script, the file can be accessed at `meta[\"\
          resources_dir\"] + \"/\" + dest`. If unspecified, `dest` will be set to\
          \ the basename of the `path` parameter.\n * path: `path/to/file`, the path\
          \ of the input file. Can be a relative or an absolute path, or a URI. Mutually\
          \ exclusive with `text`.\n * text: ...multiline text..., the content of\
          \ the resulting file specified as a string. Mutually exclusive with `path`.\n\
          \ * is_executable: `true` / `false`, whether the resulting resource file\
          \ should be made executable.\n"
        type: "array"
        items:
          $ref: "defs_viash.yaml#/definitions/Resource"
      keywords:
        description: "The keywords of the components."
        type: "array"
        items:
          type: "string"
      test_resources:
        description: "One or more scripts to be used to test the component behaviour\
          \ when `viash test` is invoked. Additional files of type `file` will be\
          \ made available only during testing. Each test script should expect no\
          \ command-line inputs, be platform-independent, and return an exit code\
          \ >0 when unexpected behaviour occurs during testing. See Unit Testing for\
          \ more info."
        type: "array"
        items:
          $ref: "defs_viash.yaml#/definitions/Resource"
      namespace:
        description: "Namespace this component is a part of. See the Namespaces guide\
          \ for more information on namespaces."
        type: "string"
      arguments:
        description: "A list of arguments for this component. For each argument, a\
          \ type and a name must be specified. Depending on the type of argument,\
          \ different properties can be set. See these reference pages per type for\
          \ more information:  \n\n - string\n - file\n - integer\n - double\n - boolean\n\
          \ - boolean_true\n - boolean_false\n"
        type: "array"
        items:
          $ref: "defs_viash.yaml#/definitions/Argument"
      __merge__:
        $ref: "#/definitions/Merge"
    required:
    - "name"
    additionalProperties: false
  Merge:
    type: string
    description: Path to a YAML file to inherit values from.
    oneOf:
      - type: array
      - type: string
  FileFormat:
    description: 'File format metadata'
    type: object
    required: [label, file_format]
    properties:
      label:
        $ref: "defs_common.yaml#/definitions/Label"
      summary: 
        $ref: "defs_common.yaml#/definitions/Summary"
      file_format:
        oneOf:
          - type: object
            required: [type]
            additionalProperties: false
            properties:
              type:
                const: h5ad
              X:
                $ref: "#/definitions/AnnDataSlot"
              layers:
                type: array
                items:
                  $ref: "#/definitions/AnnDataSlot"
              var:
                type: array
                items:
                  $ref: "#/definitions/AnnDataSlot"
              varm:
                type: array
                items:
                  $ref: "#/definitions/AnnDataSlot"
              varp:
                type: array
                items:
                  $ref: "#/definitions/AnnDataSlot"
              obs:
                type: array
                items:
                  $ref: "#/definitions/AnnDataSlot"
              obsm:
                type: array
                items:
                  $ref: "#/definitions/AnnDataSlot"
              obsp:
                type: array
                items:
                  $ref: "#/definitions/AnnDataSlot"
              uns:
                type: array
                items:
                  oneOf:
                    - $ref: "#/definitions/AnnDataSlot"
                    - $ref: "#/definitions/AnnDataSlotObject"
          - type: object
            required: [type, mod]
            additionalProperties: false
            properties:
              type:
                const: h5mu
              mod:
                type: object
                additionalProperties: false
                properties:
                  rna:
                    "#/definitions/AnnData"
                  atac:
                    "#/definitions/AnnData"
                  prot:
                    "#/definitions/AnnData"
                  vdj:
                    "#/definitions/AnnData"
                  vdj_t:
                    "#/definitions/AnnData"
                  vdj_b:
                    "#/definitions/AnnData"
                  gdo:
                    "#/definitions/AnnData"
                  hto:
                    "#/definitions/AnnData"
  MuData:
    required: [mod]
    additionalProperties: false
    properties:
      mod:
        type: object
        additionalProperties: false
        properties:
          rna:
            "#/definitions/AnnData"
          atac:
            "#/definitions/AnnData"
          prot:
            "#/definitions/AnnData"
          vdj:
            "#/definitions/AnnData"
          vdj_t:
            "#/definitions/AnnData"
          vdj_b:
            "#/definitions/AnnData"
          gdo:
            "#/definitions/AnnData"
          hto:
            "#/definitions/AnnData"
  AnnData:
    additionalProperties: false
    properties:
      X:
        $ref: "#/definitions/AnnDataSlot"
      layers:
        type: array
        items:
          $ref: "#/definitions/AnnDataSlot"
      var:
        type: array
        items:
          $ref: "#/definitions/AnnDataSlot"
      varm:
        type: array
        items:
          $ref: "#/definitions/AnnDataSlot"
      varp:
        type: array
        items:
          $ref: "#/definitions/AnnDataSlot"
      obs:
        type: array
        items:
          $ref: "#/definitions/AnnDataSlot"
      obsm:
        type: array
        items:
          $ref: "#/definitions/AnnDataSlot"
      obsp:
        type: array
        items:
          $ref: "#/definitions/AnnDataSlot"
      uns:
        type: array
        items:
          oneOf:
            - $ref: "#/definitions/AnnDataSlot"
            - $ref: "#/definitions/AnnDataSlotObject"
  AnnDataSlot:
    properties:
      type:
        enum: [integer, double, string, boolean]
      name:
        type: string
        description: A unique identifier.
        pattern: "^[a-zA-Z_][a-zA-Z0-9_]*$"
      description:
        type: string
      required:
        type: boolean
    required: [type, name, description, required]
  AnnDataSlotObject:
    properties:
      type:
        enum: [object]
      name:
        type: string
        description: A unique identifier.
        pattern: "^[a-zA-Z_][a-zA-Z0-9_]*$"
      description:
        type: string
      required:
        type: boolean
    required: [type, name, description, required]

  # added specific properties to the author info
  Author:
    description: Author metadata.
    type: object
    additionalProperties: false
    properties:
      name:
        description: Full name of the author, usually in the name of FirstName MiddleName LastName.
        type: string
      info:
        description: Additional information on the author
        type: object
        additionalProperties: false
        required: [role, links, organizations]
        properties:
          links:
            type: object
            additionalProperties: false
            required: github
            properties:
              github:
                type: string
              orcid:
                type: string
              email:
                type: string
              twitter:
                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