Workflow.yml

saladVersion: v1.1
$base: "https://w3id.org/cwl/cwl#"

$namespaces:
  cwl: "https://w3id.org/cwl/cwl#"
  rdfs: "http://www.w3.org/2000/01/rdf-schema#"

$graph:

- name: "WorkflowDoc"
  type: documentation
  doc:
    - |
      # Common Workflow Language (CWL) Workflow Description, v1.1

      This version:
        * https://w3id.org/cwl/v1.1/

      Current version:
        * https://w3id.org/cwl/
    - "\n\n"
    - {$include: contrib.md}
    - "\n\n"
    - |
      # Abstract

      One way to define a workflow is: an analysis task represented by a
      directed graph describing a sequence of operations that transform an
      input data set to output. This specification defines the Common Workflow
      Language (CWL) Workflow description, a vendor-neutral standard for
      representing workflows intended to be portable across a variety of
      computing platforms.

    - {$include: intro.md}

    - |

      ## Introduction to CWL Workflow standard v1.1

      This specification represents the latest stable release from the
      CWL group.  Since the v1.0 release, v1.1 introduces the
      following updates to the CWL Workflow standard.
      Documents should to use `cwlVersion: v1.1` to make use of new
      syntax and features introduced in v1.1.  Existing v1.0 documents
      should be trivially updatable by changing `cwlVersion`, however
      CWL documents that relied on previously undefined or
      underspecified behavior may have slightly different behavior in
      v1.1.

      ## Changelog

        * Clarify intent of ExpressionTool and clarify that they can be run standalone.
        * Clarify how Requirements are inherited by step processes.
        * Clarify behavior around step inputs not consumed by the target
          run process.
        * Document explicitly that CWL allows pass-through of workflow inputs to outputs.
        * Added optional name and doc fields to `OutputRecordSchema`.
        * Default values for some fields are now expressed in the schema.
        * When defining record types, fields of type `File` may now include
          `format`, `secondaryFiles`, and `streamable`.
        * The `Input` schemas (`Record`, `Array`, `Enum`),  now permits a `doc` field.
        * Any `doc` field may be an array of strings in addition to the
          previously allowed single string.
        * The `run` field now introduces a subscope so that embedded
          definitions do not have identifier conflicts with the
          outer workflow.
        * `Workflow.inputs` and `ExpressionTool.inputs` now refer to the type
          `WorkflowInputParameter` instead of `InputParameter`; the only syntax
          difference from v1.0 is that `inputBinding` is now deprecated (as
          there is no command line to bind input values to) and `inputBinding`
          in a `Workflow` context will be removed in v2.0. Use the new
          `WorkflowInputParameter.loadContents` instead.
        * The presence of `OutputRecordField.outputBinding` in v1.0 was due to
          a technical error and as it makes no semantic sense it was removed.
        * `WorkflowStepInput` now has a `label` field.
        * [Addition](#Requirements_and_hints) of `cwl:requirements` field to
          input object documents.
        * `secondaryFiles` can now be explicitly marked as `required` or not.
        * Add note that undefined details related to execution are left open to
          the platform.
        * [Added](#WorkReuse) `WorkReuse` feature, allowing to enable or disable the reuse
          behavior for a particular tool or step for implementations that
          support reusing output from past work.
        * [Added](#NetworkAccess) `NetworkAccess` feature, allowing to indicate whether a
          process requires outgoing network access.
        * [Added](#InplaceUpdateRequirement) `InplaceUpdateRequirement` feature, allowing tools to directly
          update files with `writable: true` in `InitialWorkDirRequirement`.
        * [Added](#LoadListingRequirement) `LoadListingRequirement`
          and [loadListing](#LoadContents) to control whether and how
          `Directory` listings should be loaded for use in expressions.
        * [Better explain](#map) the `map<…>` notation that has existed since v1.0.
        * Fixed schema error where the `type` field inside the `inputs` and
          `outputs` fields for both `Workflow` and `ExpressionTool` was
           incorrectly listed as optional.
        * For multi-Process CWL documents, if no particular process is named then
          the process with the `id` of `#main` is chosen.
        * [Made explicit](#Generic_execution_process) that the `$namespaces` of
          the top level CWL document are also available to the input object as
          well.
        * Fields with type "Expression" no longer include "string" in
          the type union unless a string is semantically valid.  Where
          a bare string is not semantically valid, these fields must
          contain either a non-string value accepted by the field
          type, or a valid expression which returns a value having one
          of the the other types defined for that field.
        * [WorkflowStepInput](#WorkflowStepInput) now has a `loadContents` field.
        * [WorkflowStepInput.id](#WorkflowStepInput) field value does not have to match an
          `input.id` value from the process specified in the `run` field.
        * 2021-11-22 Errata: Fixed `$schema` typo. It is `$schemas` (plural).

      See also the [CWL Command Line Tool Description, v1.1 changelog](CommandLineTool.html#Changelog).

      ## Purpose

      The Common Workflow Language Command Line Tool Description express
      workflows for data-intensive science, such as Bioinformatics, Chemistry,
      Physics, and Astronomy.  This specification is intended to define a data
      and execution model for Workflows that can be implemented on top of a
      variety of computing platforms, ranging from an individual workstation to
      cluster, grid, cloud, and high performance computing systems. Details related
      to execution of these workflow not laid out in this specification are open to
      interpretation by the computing platform implementing this specification.

    - {$include: concepts.md}

- name: ExpressionToolOutputParameter
  type: record
  extends: OutputParameter
  fields:
    - name: type
      type:
        - CWLType
        - OutputRecordSchema
        - OutputEnumSchema
        - OutputArraySchema
        - string
        - type: array
          items:
            - CWLType
            - OutputRecordSchema
            - OutputEnumSchema
            - OutputArraySchema
            - string
      jsonldPredicate:
        "_id": "sld:type"
        "_type": "@vocab"
        refScope: 2
        typeDSL: True
      doc: |
        Specify valid types of data that may be assigned to this parameter.


- name: WorkflowInputParameter
  type: record
  extends: InputParameter
  docParent: "#Workflow"
  fields:
    - name: type
      type:
        - CWLType
        - InputRecordSchema
        - InputEnumSchema
        - InputArraySchema
        - string
        - type: array
          items:
            - CWLType
            - InputRecordSchema
            - InputEnumSchema
            - InputArraySchema
            - string
      jsonldPredicate:
        "_id": "sld:type"
        "_type": "@vocab"
        refScope: 2
        typeDSL: True
      doc: |
        Specify valid types of data that may be assigned to this parameter.
    - name: inputBinding
      type: InputBinding?
      doc: |
        Deprecated.  Preserved for v1.0 backwards compatability.  Will be removed in
        CWL v2.0.  Use `WorkflowInputParameter.loadContents` instead.
      jsonldPredicate: "cwl:inputBinding"


- type: record
  name: ExpressionTool
  extends: Process
  specialize:
    - specializeFrom: InputParameter
      specializeTo: WorkflowInputParameter
    - specializeFrom: OutputParameter
      specializeTo: ExpressionToolOutputParameter
  documentRoot: true
  doc: |
    An ExpressionTool is a type of Process object that can be run by itself
    or as a Workflow step. It executes a pure Javascript expression that has
    access to the same input parameters as a workflow. It is meant to be used
    sparingly as a way to isolate complex Javascript expressions that need to
    operate on input data and produce some result; perhaps just a
    rearrangement of the inputs. No Docker software container is required
    or allowed.
  fields:
    - name: class
      jsonldPredicate:
        "_id": "@type"
        "_type": "@vocab"
      type: string
    - name: expression
      type: Expression
      doc: |
        The expression to execute.  The expression must return a JSON object which
        matches the output parameters of the ExpressionTool.

- name: LinkMergeMethod
  type: enum
  docParent: "#WorkflowStepInput"
  doc: The input link merge method, described in [WorkflowStepInput](#WorkflowStepInput).
  symbols:
    - merge_nested
    - merge_flattened


- name: WorkflowOutputParameter
  type: record
  extends: OutputParameter
  docParent: "#Workflow"
  doc: |
    Describe an output parameter of a workflow.  The parameter must be
    connected to one or more parameters 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 one or more workflow parameters that supply the value of to
        the output parameter.
      jsonldPredicate:
        "_id": "cwl:outputSource"
        "_type": "@id"
        refScope: 0
      type:
        - string?
        - string[]?
    - name: linkMerge
      type: ["null", LinkMergeMethod]
      jsonldPredicate: "cwl:linkMerge"
      default: merge_nested
      doc: |
        The method to use to merge multiple sources into a single array.
        If not specified, the default method is "merge_nested".
    - name: type
      type:
        - CWLType
        - OutputRecordSchema
        - OutputEnumSchema
        - OutputArraySchema
        - string
        - type: array
          items:
            - CWLType
            - OutputRecordSchema
            - OutputEnumSchema
            - OutputArraySchema
            - string
      jsonldPredicate:
        "_id": "sld:type"
        "_type": "@vocab"
        refScope: 2
        typeDSL: True
      doc: |
        Specify valid types of data that may be assigned to this parameter.


- 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[]?
    - name: linkMerge
      type: LinkMergeMethod?
      jsonldPredicate: "cwl:linkMerge"
      default: merge_nested
      doc: |
        The method to use to merge multiple inbound links into a single array.
        If not specified, the default method is "merge_nested".


- type: record
  name: WorkflowStepInput
  extends: [Identified, Sink, LoadContents, Labeled]
  docParent: "#WorkflowStep"
  doc: |
    The input of a workflow step connects an upstream parameter (from the
    workflow inputs, or the outputs of other workflows steps) with the input
    parameters of the process specified by the `run` field. Only input parameters
    declared by the target process will be passed through at runtime to the process
    though additonal parameters may be specified (for use within `valueFrom`
    expressions for instance) - unconnected or unused parameters do not represent an
    error condition.

    ## Input object

    A WorkflowStepInput object must contain an `id` field in the form
    `#fieldname` or `#prefix/fieldname`.  When the `id` field contains a slash
    `/` the field name consists of the characters following the final slash
    (the prefix portion may contain one or more slashes to indicate scope).
    This defines a field of the workflow step input object with the value of
    the `source` parameter(s).

    ## Merging

    To merge multiple inbound data links,
    [MultipleInputFeatureRequirement](#MultipleInputFeatureRequirement) must be specified
    in the workflow or workflow step requirements.

    If the sink parameter is an array, or named in a [workflow
    scatter](#WorkflowStep) operation, there may be multiple inbound data links
    listed in the `source` field.  The values from the input links are merged
    depending on the method specified in the `linkMerge` field.  If not
    specified, the default method is "merge_nested".

    * **merge_nested**

      The input must be an array consisting of exactly one entry for each
      input link.  If "merge_nested" is specified with a single link, the value
      from the link must be wrapped in a single-item list.

    * **merge_flattened**

      1. The source and sink parameters must be compatible types, or the source
         type must be compatible with single element from the "items" type of
         the destination array parameter.
      2. Source parameters which are arrays are concatenated.
         Source parameters which are single element types are appended as
         single elements.

  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
    - name: valueFrom
      type:
        - "null"
        - string
        - Expression
      jsonldPredicate: "cwl:valueFrom"
      doc: |
        To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must
        be specified in the workflow or workflow step requirements.

        If `valueFrom` is a constant string value, use this as the value for
        this input parameter.

        If `valueFrom` is a parameter reference or expression, it must be
        evaluated to yield the actual value to be assiged to the input field.

        The `self` value in the parameter reference or expression must be
        1. `null` if there is no `source` field
        2. the value of the parameter(s) specified in the `source` field when this
        workflow input parameter **is not** specified in this workflow step's `scatter` field.
        3. an element of the parameter specified in the `source` field when this workflow input
        parameter **is** specified in this workflow step's `scatter` field.

        The value of `inputs` in the parameter reference or expression must be
        the input object to the workflow step after assigning the `source`
        values, applying `default`, and then scattering.  The order of
        evaluating `valueFrom` among step input parameters is undefined and the
        result of evaluating `valueFrom` on a parameter must not be visible to
        evaluation of `valueFrom` on other parameters.


- type: record
  name: WorkflowStepOutput
  docParent: "#WorkflowStep"
  extends: 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.


- name: ScatterMethod
  type: enum
  docParent: "#WorkflowStep"
  doc: The scatter method, as described in [workflow step scatter](#WorkflowStep).
  symbols:
    - dotproduct
    - nested_crossproduct
    - flat_crossproduct


- name: WorkflowStep
  type: record
  extends: [Identified, Labeled, sld:Documented]
  docParent: "#Workflow"
  doc: |
    A workflow step is an executable element of a workflow.  It specifies the
    underlying process implementation (such as `CommandLineTool` or another
    `Workflow`) in the `run` field and connects the input and output parameters
    of the underlying process to workflow parameters.

    # Scatter/gather

    To use scatter/gather,
    [ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified
    in the workflow or workflow step requirements.

    A "scatter" operation specifies that the associated workflow step or
    subworkflow should execute separately over a list of input elements.  Each
    job making up a scatter operation is independent and may be executed
    concurrently.

    The `scatter` field specifies one or more input parameters which will be
    scattered.  An input parameter may be listed more than once.  The declared
    type of each input parameter is implicitly becomes an array of items of the
    input parameter type.  If a parameter is listed more than once, it becomes
    a nested array.  As a result, upstream parameters which are connected to
    scattered parameters must be arrays.

    All output parameter types are also implicitly wrapped in arrays.  Each job
    in the scatter results in an entry in the output array.

    If any scattered parameter runtime value is an empty array, all outputs are
    set to empty arrays and no work is done for the step, according to
    applicable scattering rules.

    If `scatter` declares more than one input parameter, `scatterMethod`
    describes how to decompose the input into a discrete set of jobs.

      * **dotproduct** specifies that each of the input arrays are aligned and one
          element taken from each array to construct each job.  It is an error
          if all input arrays are not the same length.

      * **nested_crossproduct** specifies the Cartesian product of the inputs,
          producing a job for every combination of the scattered inputs.  The
          output must be nested arrays for each level of scattering, in the
          order that the input arrays are listed in the `scatter` field.

      * **flat_crossproduct** specifies the Cartesian product of the inputs,
          producing a job for every combination of the scattered inputs.  The
          output arrays must be flattened to a single level, but otherwise listed in the
          order that the input arrays are listed in the `scatter` field.

    # Subworkflows

    To specify a nested workflow as part of a workflow step,
    [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) must be
    specified in the workflow or workflow step requirements.

    It is a fatal error if a workflow directly or indirectly invokes itself as
    a subworkflow (recursive workflows are not allowed).

  fields:
    - name: in
      type: WorkflowStepInput[]
      jsonldPredicate:
        _id: "cwl: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]
      jsonldPredicate:
        _id: "cwl:out"
        _type: "@id"
        identity: true
      doc: |
        Defines the parameters representing the output of the process.  May be
        used to generate and/or validate the output object.
    - name: requirements
      type: ProcessRequirement[]?
      jsonldPredicate:
        _id: "cwl:requirements"
        mapSubject: class
      doc: |
        Declares requirements that apply to either the runtime environment or the
        workflow engine that must be met in order to execute this workflow step.  If
        an implementation cannot satisfy all requirements, or a requirement is
        listed which is not recognized by the implementation, it is a fatal
        error and the implementation must not attempt to run the process,
        unless overridden at user option.
    - name: hints
      type: Any[]?
      jsonldPredicate:
        _id: "cwl:hints"
        noLinkCheck: true
        mapSubject: class
      doc: |
        Declares hints applying to either the runtime environment or the
        workflow engine that may be helpful in executing this workflow step.  It is
        not an error if an implementation cannot satisfy all hints, however
        the implementation may report a warning.
    - name: run
      type: [string, Process]
      jsonldPredicate:
        _id: "cwl:run"
        _type: "@id"
        subscope: run
      doc: |
        Specifies the process to run.
    - name: scatter
      type:
        - string?
        - string[]?
      jsonldPredicate:
        "_id": "cwl:scatter"
        "_type": "@id"
        "_container": "@list"
        refScope: 0
    - name: scatterMethod
      doc: |
        Required if `scatter` is an array of more than one element.
      type: ScatterMethod?
      jsonldPredicate:
        "_id": "cwl:scatterMethod"
        "_type": "@vocab"


- name: Workflow
  type: record
  extends: "#Process"
  documentRoot: true
  specialize:
    - specializeFrom: InputParameter
      specializeTo: WorkflowInputParameter
    - specializeFrom: OutputParameter
      specializeTo: WorkflowOutputParameter
  doc: |
    A workflow describes a set of **steps** and the **dependencies** between
    those steps.  When a step produces output that will be consumed by a
    second step, the first step is a dependency of the second step.

    When there is a dependency, the workflow engine must execute the preceding
    step and wait for it to successfully produce output before executing the
    dependent step.  If two steps are defined in the workflow graph that
    are not directly or indirectly dependent, these steps are **independent**,
    and may execute in any order or execute concurrently.  A workflow is
    complete when all steps have been executed.

    Dependencies between parameters are expressed using the `source` field on
    [workflow step input parameters](#WorkflowStepInput) and [workflow output
    parameters](#WorkflowOutputParameter).

    The `source` field expresses the dependency of one parameter on another
    such that when a value is associated with the parameter specified by
    `source`, that value is propagated to the destination parameter.  When all
    data links inbound to a given step are fufilled, the step is ready to
    execute.

    ## Workflow success and failure

    A completed step must result in one of `success`, `temporaryFailure` or
    `permanentFailure` states.  An implementation may choose to retry a step
    execution which resulted in `temporaryFailure`.  An implementation may
    choose to either continue running other steps of a workflow, or terminate
    immediately upon `permanentFailure`.

    * If any step of a workflow execution results in `permanentFailure`, then
    the workflow status is `permanentFailure`.

    * If one or more steps result in `temporaryFailure` and all other steps
    complete `success` or are not executed, then the workflow status is
    `temporaryFailure`.

    * If all workflow steps are executed and complete with `success`, then the
    workflow status is `success`.

    # Extensions

    [ScatterFeatureRequirement](#ScatterFeatureRequirement) and
    [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) are
    available as standard [extensions](#Extensions_and_Metadata) to core
    workflow semantics.

  fields:
    - name: "class"
      jsonldPredicate:
        "_id": "@type"
        "_type": "@vocab"
      type: string
    - name: steps
      doc: |
        The individual steps that make up the workflow.  Each step is executed when all of its
        input data links are fufilled.  An implementation may choose to execute
        the steps in a different order than listed and/or execute steps
        concurrently, provided that dependencies between steps are met.
      type:
        - type: array
          items: "#WorkflowStep"
      jsonldPredicate:
          mapSubject: id


- type: record
  name: SubworkflowFeatureRequirement
  extends: ProcessRequirement
  doc: |
    Indicates that the workflow platform must support nested workflows in
    the `run` field of [WorkflowStep](#WorkflowStep).
  fields:
    - name: "class"
      type: "string"
      doc: "Always 'SubworkflowFeatureRequirement'"
      jsonldPredicate:
        "_id": "@type"
        "_type": "@vocab"

- name: ScatterFeatureRequirement
  type: record
  extends: ProcessRequirement
  doc: |
    Indicates that the workflow platform must support the `scatter` and
    `scatterMethod` fields of [WorkflowStep](#WorkflowStep).
  fields:
    - name: "class"
      type: "string"
      doc: "Always 'ScatterFeatureRequirement'"
      jsonldPredicate:
        "_id": "@type"
        "_type": "@vocab"

- name: MultipleInputFeatureRequirement
  type: record
  extends: ProcessRequirement
  doc: |
    Indicates that the workflow platform must support multiple inbound data links
    listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput).
  fields:
    - name: "class"
      type: "string"
      doc: "Always 'MultipleInputFeatureRequirement'"
      jsonldPredicate:
        "_id": "@type"
        "_type": "@vocab"

- type: record
  name: StepInputExpressionRequirement
  extends: ProcessRequirement
  doc: |
    Indicate that the workflow platform must support the `valueFrom` field
    of [WorkflowStepInput](#WorkflowStepInput).
  fields:
    - name: "class"
      type: "string"
      doc: "Always 'StepInputExpressionRequirement'"
      jsonldPredicate:
        "_id": "@type"
        "_type": "@vocab"