workflow.yml

saladVersion: v1.1
$base: "https://galaxyproject.org/gxformat2/v19_09#"

$namespaces:
  gxformat2: "https://galaxyproject.org/gxformat2/v19_09#"
  gxformat2common: "https://galaxyproject.org/gxformat2/gxformat2common#"
  cwl: "https://w3id.org/cwl/cwl#"
  sld: "https://w3id.org/cwl/salad#"
  rdfs: "http://www.w3.org/2000/01/rdf-schema#"

$graph:
- name: "WorkflowDoc"
  type: documentation
  doc:
    - |
      # Galaxy Workflow Format 2 Description

      The traditional Galaxy workflow description (.ga) is not meant to be concise and is neither readily human readable or human writable.
      Format 2 addresses all three of these limitations while also converging (where it makes sense without sacrificing these other goals)
      with the workflow description with that used by the Common Workflow Language.

      This standard is in active development and a moving target in many ways, but we will try to keep what is ingestible by Galaxy
      backward-compatible going forward.

- $import: "../common/metaschema/metaschema_base.yml"
- $import: "./Process.yml"  # trimmed down version of cwl's Process.yml
- $import: "../common/common.yml"

- name: GalaxyType
  type: enum
  extends: sld:PrimitiveType
  symbols:
    - integer
    - text
    - File
    - data
    - collection
  doc:
    - "Extends primitive types with the native Galaxy concepts such datasets and collections."
    - "integer: an alias for int type - matches syntax used by Galaxy tools"
    - "text: an alias for string type - matches syntax used by Galaxy tools"
    - "File: an alias for data - there are subtle differences between a plain file, the CWL concept of 'File', and the Galaxy concept of a dataset - this may have subtly difference semantics in the future"
    - "data: a Galaxy dataset"
    - "collection: a Galaxy dataset collection"

- name: WorkflowStepType
  type: enum
  symbols:
    - tool
    - subworkflow
    - pause
  doc:
    - |
        Module types used by Galaxy steps. Galaxy's native format allows additional types such as data_input, data_input_collection, and parameter_type
        but these should be represented as ``inputs`` in Format2.
    - "tool: Run a tool."
    - "subworkflow: Run a subworkflow."
    - "pause: Pause computation on this branch of workflow until user allows it to continue."

- name: WorkflowInputParameter
  type: record
  extends:
    - cwl:InputParameter
    - gxformat2common:HasStepPosition
  docParent: "#GalaxyWorkflow"
  fields:
    - name: type
      type:
      - GalaxyType
      - string
      - "null"
      default: data
      jsonldPredicate:
        "_id": "sld:type"
        "_type": "@vocab"
        refScope: 2
        typeDSL: True
      doc: |
        Specify valid types of data that may be assigned to this parameter.
    - name: optional
      type:
      - boolean
      - "null"
      default: false
      doc: |
        If set to true, `WorkflowInputParameter` is not required to submit the workflow.
    - name: format
      doc: |
        Specify datatype extension for valid input datasets.
      type:
        - "null"
        - type: array
          items: string
    - name: collection_type
      doc: |
        Collection type (defaults to `list` if `type` is `collection`). Nested
        collection types are separated with colons, e.g. `list:list:paired`.
      type:
        - "null"
        - string

- name: WorkflowOutputParameter
  type: record
  extends: cwl:OutputParameter
  docParent: "#GalaxyWorkflow"
  doc: |
    Describe an output parameter of a workflow.  The parameter must be
    connected to one parameter defined in the workflow that
    will provide the value of the output parameter. It is legal to
    connect a WorkflowInputParameter to a WorkflowOutputParameter.
  fields:
    - name: outputSource
      doc: |
        Specifies workflow parameter that supply the value of to
        the output parameter.
      # Steps don't reference outputs in gxformat2 (yet anyway).
      # Can we just link the step if before the /
      #jsonldPredicate:
      #  "_id": "gxformat2:outputSource"
      #  "_type": "@id"
      #  refScope: 0
      type:
        - string?
    - name: type
      type: GalaxyType?
      default: data
      jsonldPredicate:
        "_id": "sld:type"
        "_type": "@vocab"
        refScope: 2
        typeDSL: True
      doc: |
        Specify valid types of data that may be assigned to this parameter.

- name: WorkflowStep
  type: record
  extends:
    - cwl:Identified
    - cwl:Labeled
    - sld:Documented
    - gxformat2common:HasStepPosition
    - gxformat2common:ReferencesTool
    - gxformat2common:HasStepErrors
    - gxformat2common:HasUUID
  docParent: "#GalaxyWorkflow"
  doc: |
    This represents a non-input step a Galaxy Workflow.

    # A note about `state` and `tool_state` fields.

    Only one or the other should be specified. These are two ways to represent the "state"
    of a tool at this workflow step. Both are essentially maps from parameter names to
    parameter values.

    `tool_state` is much more low-level and expects a flat dictionary with each value a JSON
    dump. Nested tool structures such as conditionals and repeats should have all their values
    in the JSON dumped string. In general `tool_state` may be present in workflows exported from
    Galaxy but shouldn't be written by humans.

    `state` can contained a typed map. Repeat values can be represented as YAML arrays. An alternative
    to representing `state` this way is defining inputs with default values.
  fields:
    - name: in
      type:  WorkflowStepInput[]?
      jsonldPredicate:
        _id: "gxformat2:in"
        mapSubject: id
        mapPredicate: source
      doc: |
        Defines the input parameters of the workflow step.  The process is ready to
        run when all required input parameters are associated with concrete
        values.  Input parameters include a schema for each parameter which is
        used to validate the input object.  It may also be used build a user
        interface for constructing the input object.
    - name: out
      type:
        - type: array
          items: [string, WorkflowStepOutput]
        - "null"
      jsonldPredicate:
        _id: "gxformat2:out"
        mapSubject: id
        mapPredicate: source
      doc: |
        Defines the parameters representing the output of the process.  May be
        used to generate and/or validate the output object.

        This can also be called 'outputs' for legacy reasons - but the resulting
        workflow document is not a valid instance of this schema.
    - name: state
      type: Any?
      doc: |
        Structured tool state.
      jsonldPredicate:
        _id: "gxformat2:state"
        noLinkCheck: true
    - name: tool_state
      type: Any?
      jsonldPredicate:
        _id: "gxformat2:tool_state"
        noLinkCheck: true
      doc: |
        Unstructured tool state.
    - name: type
      type: WorkflowStepType?
      jsonldPredicate:
        "_id": "sld:type"
        "_type": "@vocab"
        refScope: 2
        typeDSL: True
      default: tool
      doc: |
        Workflow step module's type (defaults to 'tool').
    - name: run
      type:
        - "null"
        - GalaxyWorkflow
      jsonldPredicate:
        _id: "cwl:run"
        _type: "@id"
        subscope: run
      doc: |
        Specifies a subworkflow to run.
    - name: runtime_inputs
      type:
        - "null"
        - type: array
          items: string
    - name: when
      type:
        - "null"
        - string  # TODO: cwl defines an enum for this, not sure how that works
      jsonldPredicate:
        _id: "gxformat2:when"
        noLinkCheck: true
      doc: |
        If defined, only run the step when the expression evaluates to
        `true`.  If `false` the step is skipped.  A skipped step
        produces a `null` on each output.

        Expression should be an ecma5.1 expression.

- name: Sink
  type: record
  abstract: true
  fields:
    - name: source
      doc: |
        Specifies one or more workflow parameters that will provide input to
        the underlying step parameter.
      jsonldPredicate:
        "_id": "cwl:source"
        "_type": "@id"
        refScope: 2
      type:
        - string?
        - string[]?

- type: record
  name: WorkflowStepInput
  extends: [cwl:Identified, Sink, cwl:Labeled]
  docParent: "#WorkflowStep"
  doc: |
    TODO:

  fields:
    - name: default
      type: ["null", Any]
      doc: |
        The default value for this parameter to use if either there is no
        `source` field, or the value produced by the `source` is `null`.  The
        default must be applied prior to scattering or evaluating `valueFrom`.
      jsonldPredicate:
        _id: "sld:default"
        noLinkCheck: true

- type: record
  name: Report
  doc: |
    Definition of an invocation report for this workflow. Currently the only
    field is 'markdown'.
  fields:
    - name: markdown
      type: string
      doc: |
        Galaxy flavored Markdown to define an invocation report.

- type: record
  name: WorkflowStepOutput
  docParent: "#WorkflowStep"
  extends: cwl:Identified
  doc: |
    Associate an output parameter of the underlying process with a workflow
    parameter.  The workflow parameter (given in the `id` field) be may be used
    as a `source` to connect with input parameters of other workflow steps, or
    with an output parameter of the process.

    A unique identifier for this workflow output parameter.  This is
    the identifier to use in the `source` field of `WorkflowStepInput`
    to connect the output value to downstream parameters.
  fields:
    rename:
      type: string?
    hide:
      type: boolean?
    delete_intermediate_datasets:
      type: boolean?
    change_datatype:
      type: string?
    set_columns:
      type:
        - "null"
        - type: array
          items: string
    add_tags:
      type:
        - "null"
        - type: array
          items: string
    remove_tags:
      type:
        - "null"
        - type: array
          items: string

- name: GalaxyWorkflow
  type: record
  extends:
    - cwl:Process
    - gxformat2common:HasUUID
  specialize:
    - specializeFrom: cwl:InputParameter
      specializeTo: WorkflowInputParameter
    - specializeFrom: cwl:OutputParameter
      specializeTo: WorkflowOutputParameter
  documentRoot: true
  doc: |
    A Galaxy workflow description. This record corresponds to the description of a workflow that should be executable
    on a Galaxy server that includes the contained tool definitions.

    The workflows API or the user interface of Galaxy instances that are of version 19.09 or newer should be able to
    import a document defining this record.

    ## A note about `label` field.

    This is the name of the workflow in the Galaxy user interface. This is the mechanism that
    users will primarily identify the workflow using. Legacy support - this may also be called 'name' and Galaxy will
    consume the workflow document fine and treat this attribute correctly - however in order to validate against this
    workflow definition schema the attribute should be called `label`.
  fields:
    # I can't find a way to override the documentation of label, even though I contextual.
    # - name: label
    #  type:
    #    - "null"
    #    - string
    #  jsonldPredicate: "rdfs:label"
    #  doc: {$include: ../common/workflow_label_description.txt}
    #  # Legacy support - this may also be called 'name' and Galaxy will consume the workflow fine and treat this
    #  # attribute correctly - however in order to validate against this schema the attribute should be called label.
    - name: "class"
      jsonldPredicate:
        "_id": "@type"
        "_type": "@vocab"
      type: string
    - name: steps
      doc: {$include: ../common/steps_description.txt}
      type:
        - type: array
          items: "#WorkflowStep"
      jsonldPredicate:
          mapSubject: id
    - name: report
      doc: Workflow invocation report template.
      type: Report?
    - name: tags
      type:
      - type: array
        items: string
      - "null"
      doc: |
        Tags for the workflow.
    - name: creator
      type: Any?
      doc: Can be a schema.org Person (https://schema.org/Person) or Organization (https://schema.org/Organization) entity
    - name: license
      type: string?
      doc: Must be a valid license listed at https://spdx.org/licenses/
    - name: release
      type: string?
      doc: If listed should correspond to the release of the workflow in its source reposiory.