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This profile uses terminology from the [RO-Crate 1.1 specification](https://w3id.org/ro/crate/1.1), and [extends it](https://www.researchobject.org/ro-crate/1.1/appendix/jsonld.html#extending-ro-crate) with additional terms from the [workflow-run](https://github.com/ResearchObject/ro-terms/tree/master/workflow-run) ro-terms namespace.
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}
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```
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Note that the command line shown in the action's `description` is not directly re-executable, as file paths are not required to match the RO-Crate locations. For a more structural and reproducible description of tool executions, see [Workflow Run Crate](workflow_run_crate).
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Note that the command line shown in the action's `description` is not directly re-executable, as file paths are not required to match the RO-Crate locations. For a more structural and reproducible description of tool executions, see [Workflow Run Crate](../workflow_run_crate).
This profile uses terminology from the [RO-Crate 1.1 specification](https://w3id.org/ro/crate/1.1), and [extends it](https://www.researchobject.org/ro-crate/1.1/appendix/jsonld.html#extending-ro-crate) with additional terms from the [workflow-run](https://github.com/ResearchObject/ro-terms/tree/master/workflow-run) ro-terms namespace.
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## Overview
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This profile extends [Workflow Run Crate](workflow_run_crate) with specifications to describe internal details of the workflow run, such as step executions and intermediate outputs.
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This profile extends [Workflow Run Crate](../workflow_run_crate) with specifications to describe internal details of the workflow run, such as step executions and intermediate outputs.
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A Provenance Run Crate MUST record the details of *tool* executions orchestrated by the workflow through additional [CreateAction](http://schema.org/CreateAction) entities, each of which MUST refer to an entity representing the tool itself via [instrument](http://schema.org/instrument) as specified in [Process Run Crate](process_run_crate). Entities representing the tools MAY reference formal parameter definitions via `input` and `output` (and `environment`, in the case of [environment variables](workflow_run_crate#environment-variables-as-formal-parameters)) as specified in [Workflow Run Crate](workflow_run_crate). The workflow MUST refer to the orchestrated tools via [hasPart](http://schema.org/hasPart) (the usage of `hasPart` for this purpose follows the Bioschemas [ComputationalWorkflow profile](http://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE)).
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A Provenance Run Crate MUST record the details of *tool* executions orchestrated by the workflow through additional [CreateAction](http://schema.org/CreateAction) entities, each of which MUST refer to an entity representing the tool itself via [instrument](http://schema.org/instrument) as specified in [Process Run Crate](../process_run_crate). Entities representing the tools MAY reference formal parameter definitions via `input` and `output` (and `environment`, in the case of [environment variables](../workflow_run_crate#environment-variables-as-formal-parameters)) as specified in [Workflow Run Crate](../workflow_run_crate). The workflow MUST refer to the orchestrated tools via [hasPart](http://schema.org/hasPart) (the usage of `hasPart` for this purpose follows the Bioschemas [ComputationalWorkflow profile](http://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE)).
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The crate SHOULD also record *step* executions via [ControlAction](http://schema.org/ControlAction) instances, each of which MUST reference: a [HowToStep](http://schema.org/HowToStep) instance representing the step via `instrument`; the `CreateAction` representing the corresponding tool run via `object`. The workflow MUST reference any `HowToStep` instances that represent its steps via [step](http://schema.org/step). Each `HowToStep` instance MUST reference the entity that represents its corresponding tool via [workExample](http://schema.org/workExample), and MAY indicate its position in the execution order via [position](http://schema.org/position). In addition to `File`, `SoftwareSourceCode` and `ComputationalWorkflow`, a workflow that points to step metadata via `step` MUST have a type of [HowTo](http://schema.org/HowTo).
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```
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See also the [section on referencing configuration files of executed tools](process_run_crate#referencing-configuration-files).
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See also the [section on referencing configuration files of executed tools](../process_run_crate#referencing-configuration-files).
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## Tool wrapper dependencies
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In some workflow systems (e.g., CWL, Galaxy), tools are typically wrappers for an executable written in a scripting programming language. This MAY be represented by listing the wrapped tool and its dependencies as described in [Specifying software dependencies](process_run_crate#specifying-software-dependencies). The wrapped tool can be highlighted by using `mainEntity`:
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In some workflow systems (e.g., CWL, Galaxy), tools are typically wrappers for an executable written in a scripting programming language. This MAY be represented by listing the wrapped tool and its dependencies as described in [Specifying software dependencies](../process_run_crate#specifying-software-dependencies). The wrapped tool can be highlighted by using `mainEntity`:
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```json
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{
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## Requirements
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The requirements of this profile are those of [Workflow Run Crate](workflow_run_crate) plus the ones listed below.
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The requirements of this profile are those of [Workflow Run Crate](../workflow_run_crate) plus the ones listed below.
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<table>
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<tr>
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<td>hasPart</td>
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<td>MUST</td>
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<td>Identifiers of the <em>tools</em> (including subworkflows) orchestrated by this workflow, represented as specified in the <ahref="process_run_crate#requirements">Process Run Crate requirements</a> under "SoftwareApplication". The referenced tools MAY also incude formal parameter definitions via <code>input</code> and <code>output</code> as specified in <ahref="workflow_run_crate">Workflow Run Crate</a>. In the case of subworkflows, the type MUST include <code>ComputationalWorkflow</code></td>
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<td>Identifiers of the <em>tools</em> (including subworkflows) orchestrated by this workflow, represented as specified in the <ahref="../process_run_crate#requirements">Process Run Crate requirements</a> under "SoftwareApplication". The referenced tools MAY also incude formal parameter definitions via <code>input</code> and <code>output</code> as specified in <ahref="../workflow_run_crate">Workflow Run Crate</a>. In the case of subworkflows, the type MUST include <code>ComputationalWorkflow</code></td>
This profile uses terminology from the [RO-Crate 1.1 specification](https://w3id.org/ro/crate/1.1).
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This profile is used to describe the execution of a computational tool that has orchestrated the execution of other tools. Such a tool is represented as a [workflow](https://www.researchobject.org/ro-crate/1.1/workflows.html) that can be executed using a *Workflow Management System (WMS)*, or *workflow engine* (e.g. [cwltool](https://github.com/common-workflow-language/cwltool)).
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Workflow Run Crate is a combination of [Process Run Crate](process_run_crate) and [Workflow RO-Crate](https://w3id.org/workflowhub/workflow-ro-crate/). In particular, the RO-Crate MUST have a `ComputationalWorkflow`[mainEntity](http://schema.org/mainEntity) described according to the Workflow RO-Crate specification (*main workflow*), and `CreateAction` instances corresponding to its execution (thus having the main workflow as `instrument`) MUST be described as specified in Process Run Crate and this profile. Details regarding the execution of individual workflow steps can be described with the [Provenance Run Crate](provenance_run_crate) profile.
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Workflow Run Crate is a combination of [Process Run Crate](../process_run_crate) and [Workflow RO-Crate](https://w3id.org/workflowhub/workflow-ro-crate/). In particular, the RO-Crate MUST have a `ComputationalWorkflow`[mainEntity](http://schema.org/mainEntity) described according to the Workflow RO-Crate specification (*main workflow*), and `CreateAction` instances corresponding to its execution (thus having the main workflow as `instrument`) MUST be described as specified in Process Run Crate and this profile. Details regarding the execution of individual workflow steps can be described with the [Provenance Run Crate](../provenance_run_crate) profile.
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Workflows can have multiple input and output parameter slots that have to be mapped to actual files, directories or other values (e.g., a string or a number) before they can be executed. It is OPTIONAL to define such entities for a `ComputationalWorkflow`. If included, parameter definitions MUST be provided as [FormalParameter](https://bioschemas.org/types/FormalParameter/1.0-RELEASE) entities and referenced from the `ComputationalWorkflow` via `input` and `output` (see the [Bioschemas ComputationalWorkflow profile](https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE)).
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A data entity or `PropertyValue` that realizes a `FormalParameter` definition SHOULD refer to it via [exampleOfWork](https://schema.org/exampleOfWork); additionally, if the data entity or `PropertyValue` is an illustrative example of the parameter, the latter MAY refer back to the former using the reverse property [workExample](https://schema.org/workExample). This links the `input` of a `ComputationalWorkflow` to the `object` of a `CreateAction`, and the `output` of a `ComputationalWorkflow` to the `result` of a `CreateAction`. An `object` item that does not match a slot in the workflow's input interface (e.g., a [configuration file](process_run_crate#referencing-configuration-files) read from a predefined path) MUST NOT refer to a `FormalParameter` of the `ComputationalWorkflow` via `exampleOfWork`. A `FormalParameter` that maps to a `PropertyValue` SHOULD have a subclass of [DataType](https://schema.org/DataType) (e.g., [Integer](https://schema.org/Integer)) — or [PropertyValue](https://schema.org/PropertyValue), in the case of dictionary-like structured types — as its `additionalType`. See [CWL parameter mapping](/workflow-run-crate/cwl_param_mapping) for an example. To support reproducibility, the `name` field of a `FormalParameter` instance SHOULD match the name of the corresponding workflow parameter slot.
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A data entity or `PropertyValue` that realizes a `FormalParameter` definition SHOULD refer to it via [exampleOfWork](https://schema.org/exampleOfWork); additionally, if the data entity or `PropertyValue` is an illustrative example of the parameter, the latter MAY refer back to the former using the reverse property [workExample](https://schema.org/workExample). This links the `input` of a `ComputationalWorkflow` to the `object` of a `CreateAction`, and the `output` of a `ComputationalWorkflow` to the `result` of a `CreateAction`. An `object` item that does not match a slot in the workflow's input interface (e.g., a [configuration file](../process_run_crate#referencing-configuration-files) read from a predefined path) MUST NOT refer to a `FormalParameter` of the `ComputationalWorkflow` via `exampleOfWork`. A `FormalParameter` that maps to a `PropertyValue` SHOULD have a subclass of [DataType](https://schema.org/DataType) (e.g., [Integer](https://schema.org/Integer)) — or [PropertyValue](https://schema.org/PropertyValue), in the case of dictionary-like structured types — as its `additionalType`. See [CWL parameter mapping](/workflow-run-crate/cwl_param_mapping) for an example. To support reproducibility, the `name` field of a `FormalParameter` instance SHOULD match the name of the corresponding workflow parameter slot.
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Additional properties described in the [Bioschemas FormalParameter profile](https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE) (e.g., `defaultValue`) MAY be used to provide additional information, but strict conformance is not required. A `FormalParameter` definition that strictly conforms to the Bioschemas profile SHOULD reference the relevant versioned URL via `conformsTo`.
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## Environment variables as formal parameters
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The Process Run Crate profile specifies how to [represent environment variable settings](process_run_crate#representing-environment-variable-settings) that affected the execution of a particular action via `environment`. A workflow, in turn, MAY indicate that it is affected by a certain environment variable by using the same `environment` property and having it point to a `FormalParameter` whose `name` is equal to the variable's name. If an action corresponding to an execution of the workflow sets that variable, the `PropertyValue` SHOULD point to the `FormalParameter` via `exampleOfWork`:
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The Process Run Crate profile specifies how to [represent environment variable settings](../process_run_crate#representing-environment-variable-settings) that affected the execution of a particular action via `environment`. A workflow, in turn, MAY indicate that it is affected by a certain environment variable by using the same `environment` property and having it point to a `FormalParameter` whose `name` is equal to the variable's name. If an action corresponding to an execution of the workflow sets that variable, the `PropertyValue` SHOULD point to the `FormalParameter` via `exampleOfWork`:
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```json
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{
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## Requirements
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This profile inherits the requirements of [Process Run Crate](process_run_crate) and [Workflow RO-Crate](https://w3id.org/workflowhub/workflow-ro-crate/). Additional specifications are listed below.
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This profile inherits the requirements of [Process Run Crate](../process_run_crate) and [Workflow RO-Crate](https://w3id.org/workflowhub/workflow-ro-crate/). Additional specifications are listed below.
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<table>
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<tr>
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<td>additionalType</td>
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<td>MUST</td>
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<td>SHOULD include: <code>File</code>, <code>Dataset</code> or <code>Collection</code> if it maps to a file, directory or <ahref="process_run_crate#representing-multi-file-objects">multi-file dataset</a>, respectively; <code>PropertyValue</code> if it maps to a dictionary-like structured value (e.g. a CWL <em>record</em>); <ahref="http://schema.org/DataType">DataType</a> or one of its subtypes (e.g. <ahref="http://schema.org/Integer">Integer</a>) if it maps to a non-structured value.</td>
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<td>SHOULD include: <code>File</code>, <code>Dataset</code> or <code>Collection</code> if it maps to a file, directory or <ahref="../process_run_crate#representing-multi-file-objects">multi-file dataset</a>, respectively; <code>PropertyValue</code> if it maps to a dictionary-like structured value (e.g. a CWL <em>record</em>); <ahref="http://schema.org/DataType">DataType</a> or one of its subtypes (e.g. <ahref="http://schema.org/Integer">Integer</a>) if it maps to a non-structured value.</td>
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