$ref: '#/definitions/CWLGraphOrFile' $schema: http://json-schema.org/draft-07/schema# definitions: CommandInputArraySchema: additionalProperties: false description: Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputArraySchema properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. inputBinding: $ref: '#/definitions/CommandLineBinding' description: Describes how to turn this object into command line arguments. items: anyOf: - $ref: '#/definitions/CommandInputArraySchema' - $ref: '#/definitions/CommandInputRecordSchema' - $ref: '#/definitions/CommandInputEnumSchema' - items: anyOf: - $ref: '#/definitions/CommandInputArraySchema' - $ref: '#/definitions/CommandInputRecordSchema' - $ref: '#/definitions/CommandInputEnumSchema' - type: string type: array - type: string description: Defines the type of the array elements. label: description: A short, human-readable label of this object. type: string name: description: The identifier for this type type: string type: const: array description: Must be `array` type: string required: - items - type type: object CommandInputEnumSchema: additionalProperties: false description: Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputEnumSchema properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. inputBinding: $ref: '#/definitions/CommandLineBinding' description: Describes how to turn this object into command line arguments. label: description: A short, human-readable label of this object. type: string name: description: The identifier for this type type: string symbols: description: Defines the set of valid symbols. items: type: string type: array type: const: enum description: Must be `enum` type: string required: - symbols - type type: object CommandInputParameter: additionalProperties: false description: An input parameter for a CommandLineTool. properties: default: description: |- The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before evaluating expressions (e.g. dependent `valueFrom` fields). doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. format: anyOf: - items: type: string type: array - type: string description: |- Only valid when `type: File` or is an array of `items: File`. This must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferably defined within an ontology. If no ontology is available, file formats may be tested by exact match. id: description: The unique identifier for this object. type: string inputBinding: $ref: '#/definitions/CommandLineBinding' description: |- Describes how to turn the input parameters of a process into command line arguments. label: description: A short, human-readable label of this object. type: string loadContents: description: |- Only valid when `type: File` or is an array of `items: File`. If true, the file (or each file in the array) must be a UTF-8 text file 64 KiB or smaller, and the implementation must read the entire contents of the file (or file array) and place it in the `contents` field of the File object for use by expressions. If the size of the file is greater than 64 KiB, the implementation must raise a fatal error. type: boolean loadListing: description: |- Only valid when `type: Directory` or is an array of `items: Directory`. Specify the desired behavior for loading the `listing` field of a Directory object for use by expressions. The order of precedence for loadListing is: 1. `loadListing` on an individual parameter 2. Inherited from `LoadListingRequirement` 3. By default: `no_listing` enum: - deep_listing - no_listing - shallow_listing type: string secondaryFiles: anyOf: - $ref: '#/definitions/SecondaryFileSchema' - items: $ref: '#/definitions/SecondaryFileSchema' type: array description: |- Only valid when `type: File` or is an array of `items: File`. Provides a pattern or expression specifying files or directories that should be included alongside the primary file. Secondary files may be required or optional. When not explicitly specified, secondary files specified for `inputs` are required and `outputs` are optional. An implementation must include matching Files and Directories in the `secondaryFiles` property of the primary file. These Files and Directories must be transferred and staged alongside the primary file. An implementation may fail workflow execution if a required secondary file does not exist. If the value is an expression, the value of `self` in the expression must be the primary input or output File object to which this binding applies. The `basename`, `nameroot` and `nameext` fields must be present in `self`. For `CommandLineTool` outputs the `path` field must also be present. The expression must return a filename string relative to the path to the primary File, a File or Directory object with either `path` or `location` and `basename` fields set, or an array consisting of strings or File or Directory objects. It is legal to reference an unchanged File or Directory object taken from input as a secondaryFile. The expression may return "null" in which case there is no secondaryFile from that expression. To work on non-filename-preserving storage systems, portable tool descriptions should avoid constructing new values from `location`, but should construct relative references using `basename` or `nameroot` instead. If a value in `secondaryFiles` is a string that is not an expression, it specifies that the following pattern should be applied to the path of the primary file to yield a filename relative to the primary File: 1. If string ends with `?` character, remove the last `?` and mark the resulting secondary file as optional. 2. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 3. Append the remainder of the string to the end of the file path. streamable: description: |- Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. type: boolean type: anyOf: - $ref: '#/definitions/CommandInputArraySchema' - $ref: '#/definitions/CommandInputRecordSchema' - $ref: '#/definitions/CommandInputEnumSchema' - items: anyOf: - $ref: '#/definitions/CommandInputArraySchema' - $ref: '#/definitions/CommandInputRecordSchema' - $ref: '#/definitions/CommandInputEnumSchema' - type: string type: array - type: string description: Specify valid types of data that may be assigned to this parameter. required: - type type: object CommandInputRecordField: description: Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputRecordField oneOf: - additionalProperties: false properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. format: anyOf: - items: type: string type: array - type: string description: |- Only valid when `type: File` or is an array of `items: File`. This must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferably defined within an ontology. If no ontology is available, file formats may be tested by exact match. inputBinding: $ref: '#/definitions/CommandLineBinding' description: Describes how to turn this object into command line arguments. label: description: A short, human-readable label of this object. type: string loadContents: description: |- Only valid when `type: File` or is an array of `items: File`. If true, the file (or each file in the array) must be a UTF-8 text file 64 KiB or smaller, and the implementation must read the entire contents of the file (or file array) and place it in the `contents` field of the File object for use by expressions. If the size of the file is greater than 64 KiB, the implementation must raise a fatal error. type: boolean loadListing: description: |- Only valid when `type: Directory` or is an array of `items: Directory`. Specify the desired behavior for loading the `listing` field of a Directory object for use by expressions. The order of precedence for loadListing is: 1. `loadListing` on an individual parameter 2. Inherited from `LoadListingRequirement` 3. By default: `no_listing` enum: - deep_listing - no_listing - shallow_listing type: string name: description: The name of the field type: string secondaryFiles: anyOf: - $ref: '#/definitions/SecondaryFileSchema' - items: $ref: '#/definitions/SecondaryFileSchema' type: array description: |- Only valid when `type: File` or is an array of `items: File`. Provides a pattern or expression specifying files or directories that should be included alongside the primary file. Secondary files may be required or optional. When not explicitly specified, secondary files specified for `inputs` are required and `outputs` are optional. An implementation must include matching Files and Directories in the `secondaryFiles` property of the primary file. These Files and Directories must be transferred and staged alongside the primary file. An implementation may fail workflow execution if a required secondary file does not exist. If the value is an expression, the value of `self` in the expression must be the primary input or output File object to which this binding applies. The `basename`, `nameroot` and `nameext` fields must be present in `self`. For `CommandLineTool` outputs the `path` field must also be present. The expression must return a filename string relative to the path to the primary File, a File or Directory object with either `path` or `location` and `basename` fields set, or an array consisting of strings or File or Directory objects. It is legal to reference an unchanged File or Directory object taken from input as a secondaryFile. The expression may return "null" in which case there is no secondaryFile from that expression. To work on non-filename-preserving storage systems, portable tool descriptions should avoid constructing new values from `location`, but should construct relative references using `basename` or `nameroot` instead. If a value in `secondaryFiles` is a string that is not an expression, it specifies that the following pattern should be applied to the path of the primary file to yield a filename relative to the primary File: 1. If string ends with `?` character, remove the last `?` and mark the resulting secondary file as optional. 2. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 3. Append the remainder of the string to the end of the file path. streamable: description: |- Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. type: boolean type: anyOf: - $ref: '#/definitions/CommandInputArraySchema' - $ref: '#/definitions/CommandInputRecordSchema' - $ref: '#/definitions/CommandInputEnumSchema' - items: anyOf: - $ref: '#/definitions/CommandInputArraySchema' - $ref: '#/definitions/CommandInputRecordSchema' - $ref: '#/definitions/CommandInputEnumSchema' - type: string type: array - type: string description: The field type required: - name - type type: object - type: array items: anyOf: - $ref: '#/definitions/CommandInputArraySchema' - $ref: '#/definitions/CommandInputRecordSchema' - $ref: '#/definitions/CommandInputEnumSchema' - items: anyOf: - $ref: '#/definitions/CommandInputArraySchema' - $ref: '#/definitions/CommandInputRecordSchema' - $ref: '#/definitions/CommandInputEnumSchema' - type: string type: array - type: string description: The field type CommandInputRecordSchema: additionalProperties: false description: Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputRecordSchema properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. fields: description: Defines the fields of the record. oneOf: - items: $ref: '#/definitions/CommandInputRecordField' type: array - patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: $ref: '#/definitions/CommandInputRecordFieldMap' type: object inputBinding: $ref: '#/definitions/CommandLineBinding' description: Describes how to turn this object into command line arguments. label: description: A short, human-readable label of this object. type: string name: description: The identifier for this type type: string type: const: record description: Must be `record` type: string required: - type type: object CommandLineBinding: additionalProperties: false description: |2- When listed under `inputBinding` in the input schema, the term "value" refers to the corresponding value in the input object. For binding objects listed in `CommandLineTool.arguments`, the term "value" refers to the effective value after evaluating `valueFrom`. The binding behavior when building the command line depends on the data type of the value. If there is a mismatch between the type described by the input schema and the effective value, such as resulting from an expression evaluation, an implementation must use the data type of the effective value. - **string**: Add `prefix` and the string to the command line. - **number**: Add `prefix` and decimal representation to command line. - **boolean**: If true, add `prefix` to the command line. If false, add nothing. - **File**: Add `prefix` and the value of [`File.path`](#File) to the command line. - **Directory**: Add `prefix` and the value of [`Directory.path`](#Directory) to the command line. - **array**: If `itemSeparator` is specified, add `prefix` and the join the array into a single string with `itemSeparator` separating the items. Otherwise, first add `prefix`, then recursively process individual elements. If the array is empty, it does not add anything to command line. - **object**: Add `prefix` only, and recursively add object fields for which `inputBinding` is specified. - **null**: Add nothing. properties: itemSeparator: description: |- Join the array elements into a single string with the elements separated by `itemSeparator`. type: string loadContents: description: |- Use of `loadContents` in `InputBinding` is deprecated. Preserved for v1.0 backwards compatibility. Will be removed in CWL v2.0. Use `InputParameter.loadContents` instead. type: boolean position: description: |- The sorting key. Default position is 0. If a [CWL Parameter Reference](#Parameter_references) or [CWL Expression](#Expressions_(Optional)) is used and if the inputBinding is associated with an input parameter, then the value of `self` will be the value of the input parameter. Input parameter defaults (as specified by the `InputParameter.default` field) must be applied before evaluating the expression. Expressions must return a single value of type int or a null. type: - string - number prefix: description: Command line prefix to add before the value. type: string separate: description: |- If true (default), then the prefix and value must be added as separate command line arguments; if false, prefix and value must be concatenated into a single command line argument. type: boolean shellQuote: description: |- If `ShellCommandRequirement` is in the requirements for the current command, this controls whether the value is quoted on the command line (default is true). Use `shellQuote: false` to inject metacharacters for operations such as pipes. If `shellQuote` is true or not provided, the implementation must not permit interpretation of any shell metacharacters or directives. type: boolean valueFrom: description: |- If `valueFrom` is a constant string value, use this as the value and apply the binding rules above. If `valueFrom` is an expression, evaluate the expression to yield the actual value to use to build the command line and apply the binding rules above. If the inputBinding is associated with an input parameter, the value of `self` in the expression will be the value of the input parameter. Input parameter defaults (as specified by the `InputParameter.default` field) must be applied before evaluating the expression. If the value of the associated input parameter is `null`, `valueFrom` is not evaluated and nothing is added to the command line. When a binding is part of the `CommandLineTool.arguments` field, the `valueFrom` field is required. type: string required: [] type: object CommandLineTool: description: This defines the schema of the CWL Command Line Tool Description document. properties: arguments: description: |- Command line bindings which are not directly associated with input parameters. If the value is a string, it is used as a string literal argument. If it is an Expression, the result of the evaluation is used as an argument. items: anyOf: - $ref: '#/definitions/CommandLineBinding' - type: string type: array baseCommand: anyOf: - items: type: string type: array - type: string description: |- Specifies the program to execute. If an array, the first element of the array is the command to execute, and subsequent elements are mandatory command line arguments. The elements in `baseCommand` must appear before any command line bindings from `inputBinding` or `arguments`. If `baseCommand` is not provided or is an empty array, the first element of the command line produced after processing `inputBinding` or `arguments` must be used as the program to execute. If the program includes a path separator character it must be an absolute path, otherwise it is an error. If the program does not include a path separator, search the `$PATH` variable in the runtime environment of the workflow runner find the absolute path of the executable. class: const: CommandLineTool type: string cwlVersion: description: |- CWL document version. Always required at the document root. Not required for a Process embedded inside another Process. enum: - draft-2 - draft-3 - draft-3.dev1 - draft-3.dev2 - draft-3.dev3 - draft-3.dev4 - draft-3.dev5 - draft-4.dev1 - draft-4.dev2 - draft-4.dev3 - v1.0 - v1.0.dev4 - v1.1 - v1.1.0-dev1 - v1.2 - v1.2.0-dev1 - v1.2.0-dev2 - v1.2.0-dev3 - v1.2.0-dev4 - v1.2.0-dev5 type: string doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. hints: description: |- Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. 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. oneOf: - items: anyOf: - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' - $ref: '#/definitions/InlineJavascriptRequirement' - $ref: '#/definitions/SchemaDefRequirement' - $ref: '#/definitions/LoadListingRequirement' - $ref: '#/definitions/DockerRequirement' - $ref: '#/definitions/SoftwareRequirement' - $ref: '#/definitions/InitialWorkDirRequirement' - $ref: '#/definitions/EnvVarRequirement' - $ref: '#/definitions/ShellCommandRequirement' - $ref: '#/definitions/ResourceRequirement' - $ref: '#/definitions/WorkReuse' - $ref: '#/definitions/NetworkAccess' - $ref: '#/definitions/InplaceUpdateRequirement' - $ref: '#/definitions/ToolTimeLimit' - $ref: '#/definitions/SubworkflowFeatureRequirement' - $ref: '#/definitions/ScatterFeatureRequirement' - $ref: '#/definitions/MultipleInputFeatureRequirement' - $ref: '#/definitions/StepInputExpressionRequirement' type: array - type: object properties: InlineJavascriptRequirement: anyOf: - $ref: '#/definitions/InlineJavascriptRequirementMap' - type: object properties: {} additionalProperties: false SchemaDefRequirement: anyOf: - $ref: '#/definitions/SchemaDefRequirementMap' - type: object properties: {} additionalProperties: false LoadListingRequirement: anyOf: - $ref: '#/definitions/LoadListingRequirementMap' - type: object properties: {} additionalProperties: false DockerRequirement: anyOf: - $ref: '#/definitions/DockerRequirementMap' - type: object properties: {} additionalProperties: false SoftwareRequirement: anyOf: - $ref: '#/definitions/SoftwareRequirementMap' - type: object properties: {} additionalProperties: false InitialWorkDirRequirement: anyOf: - $ref: '#/definitions/InitialWorkDirRequirementMap' - type: object properties: {} additionalProperties: false EnvVarRequirement: anyOf: - $ref: '#/definitions/EnvVarRequirementMap' - type: object properties: {} additionalProperties: false ShellCommandRequirement: anyOf: - $ref: '#/definitions/ShellCommandRequirementMap' - type: object properties: {} additionalProperties: false ResourceRequirement: anyOf: - $ref: '#/definitions/ResourceRequirementMap' - type: object properties: {} additionalProperties: false WorkReuse: anyOf: - $ref: '#/definitions/WorkReuseMap' - type: object properties: {} additionalProperties: false NetworkAccess: anyOf: - $ref: '#/definitions/NetworkAccessMap' - type: object properties: {} additionalProperties: false InplaceUpdateRequirement: anyOf: - $ref: '#/definitions/InplaceUpdateRequirementMap' - type: object properties: {} additionalProperties: false ToolTimeLimit: anyOf: - $ref: '#/definitions/ToolTimeLimitMap' - type: object properties: {} additionalProperties: false SubworkflowFeatureRequirement: anyOf: - $ref: '#/definitions/SubworkflowFeatureRequirementMap' - type: object properties: {} additionalProperties: false ScatterFeatureRequirement: anyOf: - $ref: '#/definitions/ScatterFeatureRequirementMap' - type: object properties: {} additionalProperties: false MultipleInputFeatureRequirement: anyOf: - $ref: '#/definitions/MultipleInputFeatureRequirementMap' - type: object properties: {} additionalProperties: false StepInputExpressionRequirement: anyOf: - $ref: '#/definitions/StepInputExpressionRequirementMap' - type: object properties: {} additionalProperties: false additionalProperties: false id: description: |- The unique identifier for this object. Only useful for `$graph` at `Process` level. Should not be exposed to users in graphical or terminal user interfaces. type: string inputs: description: |- Defines the input parameters of the process. 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 to build a user interface for constructing the input object. When accepting an input object, all input parameters must have a value. If an input parameter is missing from the input object, it must be assigned a value of `null` (or the value of `default` for that parameter, if provided) for the purposes of validation and evaluation of expressions. oneOf: - items: $ref: '#/definitions/CommandInputParameter' type: array - patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: oneOf: - $ref: '#/definitions/CommandInputParameter' - anyOf: - $ref: '#/definitions/CommandInputArraySchema' - $ref: '#/definitions/CommandInputRecordSchema' - $ref: '#/definitions/CommandInputEnumSchema' - items: anyOf: - $ref: '#/definitions/CommandInputArraySchema' - $ref: '#/definitions/CommandInputRecordSchema' - $ref: '#/definitions/CommandInputEnumSchema' - type: string type: array - type: string description: Specify valid types of data that may be assigned to this parameter. - type: array items: oneOf: - type: string - $ref: '#/definitions/CommandInputParameter' type: object intent: description: |- An identifier for the type of computational operation, of this Process. Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for [`CommandLineTool`](CommandLineTool.html#CommandLineTool), [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool). If provided, then this must be an IRI of a concept node that represents the type of operation, preferably defined within an ontology. For example, in the domain of bioinformatics, one can use an IRI from the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), like [Alignment](http://edamontology.org/operation_2928), or [Clustering](http://edamontology.org/operation_3432); or a more specific Operation concept like [Split read mapping](http://edamontology.org/operation_3199). items: type: string type: array label: description: A short, human-readable label of this object. type: string outputs: description: |- Defines the parameters representing the output of the process. May be used to generate and/or validate the output object. oneOf: - items: $ref: '#/definitions/CommandOutputParameter' type: array - patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: oneOf: - $ref: '#/definitions/CommandOutputParameter' - anyOf: - $ref: '#/definitions/CommandOutputArraySchema' - $ref: '#/definitions/CommandOutputRecordSchema' - $ref: '#/definitions/CommandOutputEnumSchema' - items: anyOf: - $ref: '#/definitions/CommandOutputArraySchema' - $ref: '#/definitions/CommandOutputRecordSchema' - $ref: '#/definitions/CommandOutputEnumSchema' - type: string type: array - type: string description: Specify valid types of data that may be assigned to this parameter. - type: array items: oneOf: - type: string - $ref: '#/definitions/CommandOutputParameter' type: object permanentFailCodes: description: |- Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail. If not specified, all exit codes except 0 are considered permanent failure. items: type: number type: array requirements: description: |- Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. 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. oneOf: - items: anyOf: - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' - $ref: '#/definitions/InlineJavascriptRequirement' - $ref: '#/definitions/SchemaDefRequirement' - $ref: '#/definitions/LoadListingRequirement' - $ref: '#/definitions/DockerRequirement' - $ref: '#/definitions/SoftwareRequirement' - $ref: '#/definitions/InitialWorkDirRequirement' - $ref: '#/definitions/EnvVarRequirement' - $ref: '#/definitions/ShellCommandRequirement' - $ref: '#/definitions/ResourceRequirement' - $ref: '#/definitions/WorkReuse' - $ref: '#/definitions/NetworkAccess' - $ref: '#/definitions/InplaceUpdateRequirement' - $ref: '#/definitions/ToolTimeLimit' - $ref: '#/definitions/SubworkflowFeatureRequirement' - $ref: '#/definitions/ScatterFeatureRequirement' - $ref: '#/definitions/MultipleInputFeatureRequirement' - $ref: '#/definitions/StepInputExpressionRequirement' type: array - type: object properties: InlineJavascriptRequirement: anyOf: - $ref: '#/definitions/InlineJavascriptRequirementMap' - type: object properties: {} additionalProperties: false SchemaDefRequirement: anyOf: - $ref: '#/definitions/SchemaDefRequirementMap' - type: object properties: {} additionalProperties: false LoadListingRequirement: anyOf: - $ref: '#/definitions/LoadListingRequirementMap' - type: object properties: {} additionalProperties: false DockerRequirement: anyOf: - $ref: '#/definitions/DockerRequirementMap' - type: object properties: {} additionalProperties: false SoftwareRequirement: anyOf: - $ref: '#/definitions/SoftwareRequirementMap' - type: object properties: {} additionalProperties: false InitialWorkDirRequirement: anyOf: - $ref: '#/definitions/InitialWorkDirRequirementMap' - type: object properties: {} additionalProperties: false EnvVarRequirement: anyOf: - $ref: '#/definitions/EnvVarRequirementMap' - type: object properties: {} additionalProperties: false ShellCommandRequirement: anyOf: - $ref: '#/definitions/ShellCommandRequirementMap' - type: object properties: {} additionalProperties: false ResourceRequirement: anyOf: - $ref: '#/definitions/ResourceRequirementMap' - type: object properties: {} additionalProperties: false WorkReuse: anyOf: - $ref: '#/definitions/WorkReuseMap' - type: object properties: {} additionalProperties: false NetworkAccess: anyOf: - $ref: '#/definitions/NetworkAccessMap' - type: object properties: {} additionalProperties: false InplaceUpdateRequirement: anyOf: - $ref: '#/definitions/InplaceUpdateRequirementMap' - type: object properties: {} additionalProperties: false ToolTimeLimit: anyOf: - $ref: '#/definitions/ToolTimeLimitMap' - type: object properties: {} additionalProperties: false SubworkflowFeatureRequirement: anyOf: - $ref: '#/definitions/SubworkflowFeatureRequirementMap' - type: object properties: {} additionalProperties: false ScatterFeatureRequirement: anyOf: - $ref: '#/definitions/ScatterFeatureRequirementMap' - type: object properties: {} additionalProperties: false MultipleInputFeatureRequirement: anyOf: - $ref: '#/definitions/MultipleInputFeatureRequirementMap' - type: object properties: {} additionalProperties: false StepInputExpressionRequirement: anyOf: - $ref: '#/definitions/StepInputExpressionRequirementMap' - type: object properties: {} additionalProperties: false additionalProperties: false stderr: description: |- Capture the command's standard error stream to a file written to the designated output directory. If `stderr` is a string, it specifies the file name to use. If `stderr` is an expression, the expression is evaluated and must return a string with the file name to use to capture stderr. If the return value is not a string, or the resulting path contains illegal characters (such as the path separator `/`) it is an error. type: string stdin: description: |- A path to a file whose contents must be piped into the command's standard input stream. type: string stdout: description: |- Capture the command's standard output stream to a file written to the designated output directory. If the `CommandLineTool` contains logically chained commands (e.g. `echo a && echo b`) `stdout` must include the output of every command. If `stdout` is a string, it specifies the file name to use. If `stdout` is an expression, the expression is evaluated and must return a string with the file name to use to capture stdout. If the return value is not a string, or the resulting path contains illegal characters (such as the path separator `/`) it is an error. type: string successCodes: description: |- Exit codes that indicate the process completed successfully. If not specified, only exit code 0 is considered success. items: type: number type: array temporaryFailCodes: description: |- Exit codes that indicate the process failed due to a possibly temporary condition, where executing the process with the same runtime environment and inputs may produce different results. If not specified, no exit codes are considered temporary failure. items: type: number type: array required: - class - inputs - outputs type: object CommandOutputArraySchema: additionalProperties: false description: Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputArraySchema properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. items: anyOf: - $ref: '#/definitions/CommandOutputArraySchema' - $ref: '#/definitions/CommandOutputRecordSchema' - $ref: '#/definitions/CommandOutputEnumSchema' - items: anyOf: - $ref: '#/definitions/CommandOutputArraySchema' - $ref: '#/definitions/CommandOutputRecordSchema' - $ref: '#/definitions/CommandOutputEnumSchema' - type: string type: array - type: string description: Defines the type of the array elements. label: description: A short, human-readable label of this object. type: string name: description: The identifier for this type type: string type: const: array description: Must be `array` type: string required: - items - type type: object CommandOutputBinding: additionalProperties: false description: |- Describes how to generate an output parameter based on the files produced by a CommandLineTool. The output parameter value is generated by applying these operations in the following order: - glob - loadContents - outputEval - secondaryFiles properties: glob: anyOf: - items: type: string type: array - type: string description: |- Find files or directories relative to the output directory, using POSIX glob(3) pathname matching. If an array is provided, find files or directories that match any pattern in the array. If an expression is provided, the expression must return a string or an array of strings, which will then be evaluated as one or more glob patterns. Must only match and return files/directories which actually exist. If the value of glob is a relative path pattern (does not begin with a slash '/') then it is resolved relative to the output directory. If the value of the glob is an absolute path pattern (it does begin with a slash '/') then it must refer to a path within the output directory. It is an error if any glob resolves to a path outside the output directory. Specifically this means globs that resolve to paths outside the output directory are illegal. A glob may match a path within the output directory which is actually a symlink to another file. In this case, the expected behavior is for the resulting File/Directory object to take the `basename` (and corresponding `nameroot` and `nameext`) of the symlink. The `location` of the File/Directory is implementation dependent, but logically the File/Directory should have the same content as the symlink target. Platforms may stage output files/directories to cloud storage that lack the concept of a symlink. In this case file content and directories may be duplicated, or (to avoid duplication) the File/Directory `location` may refer to the symlink target. It is an error if a symlink in the output directory (or any symlink in a chain of links) refers to any file or directory that is not under an input or output directory. Implementations may shut down a container before globbing output, so globs and expressions must not assume access to the container filesystem except for declared input and output. loadContents: description: |- Only valid when `type: File` or is an array of `items: File`. If true, the file (or each file in the array) must be a UTF-8 text file 64 KiB or smaller, and the implementation must read the entire contents of the file (or file array) and place it in the `contents` field of the File object for use by expressions. If the size of the file is greater than 64 KiB, the implementation must raise a fatal error. type: boolean loadListing: description: |- Only valid when `type: Directory` or is an array of `items: Directory`. Specify the desired behavior for loading the `listing` field of a Directory object for use by expressions. The order of precedence for loadListing is: 1. `loadListing` on an individual parameter 2. Inherited from `LoadListingRequirement` 3. By default: `no_listing` enum: - deep_listing - no_listing - shallow_listing type: string outputEval: description: |- Evaluate an expression to generate the output value. If `glob` was specified, the value of `self` must be an array containing file objects that were matched. If no files were matched, `self` must be a zero length array; if a single file was matched, the value of `self` is an array of a single element. The exit code of the process is available in the expression as `runtime.exitCode`. Additionally, if `loadContents` is true, the file must be a UTF-8 text file 64 KiB or smaller, and the implementation must read the entire contents of the file (or file array) and place it in the `contents` field of the File object for use in `outputEval`. If the size of the file is greater than 64 KiB, the implementation must raise a fatal error. If a tool needs to return a large amount of structured data to the workflow, loading the output object from `cwl.output.json` bypasses `outputEval` and is not subject to the 64 KiB `loadContents` limit. type: string required: [] type: object CommandOutputEnumSchema: additionalProperties: false description: Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputEnumSchema properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. label: description: A short, human-readable label of this object. type: string name: description: The identifier for this type type: string symbols: description: Defines the set of valid symbols. items: type: string type: array type: const: enum description: Must be `enum` type: string required: - symbols - type type: object CommandOutputParameter: additionalProperties: false description: An output parameter for a CommandLineTool. properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. format: description: |- Only valid when `type: File` or is an array of `items: File`. This is the file format that will be assigned to the output File object. type: string id: description: The unique identifier for this object. type: string label: description: A short, human-readable label of this object. type: string outputBinding: $ref: '#/definitions/CommandOutputBinding' description: Describes how to generate this output object based on the files produced by a CommandLineTool secondaryFiles: anyOf: - $ref: '#/definitions/SecondaryFileSchema' - items: $ref: '#/definitions/SecondaryFileSchema' type: array description: |- Only valid when `type: File` or is an array of `items: File`. Provides a pattern or expression specifying files or directories that should be included alongside the primary file. Secondary files may be required or optional. When not explicitly specified, secondary files specified for `inputs` are required and `outputs` are optional. An implementation must include matching Files and Directories in the `secondaryFiles` property of the primary file. These Files and Directories must be transferred and staged alongside the primary file. An implementation may fail workflow execution if a required secondary file does not exist. If the value is an expression, the value of `self` in the expression must be the primary input or output File object to which this binding applies. The `basename`, `nameroot` and `nameext` fields must be present in `self`. For `CommandLineTool` outputs the `path` field must also be present. The expression must return a filename string relative to the path to the primary File, a File or Directory object with either `path` or `location` and `basename` fields set, or an array consisting of strings or File or Directory objects. It is legal to reference an unchanged File or Directory object taken from input as a secondaryFile. The expression may return "null" in which case there is no secondaryFile from that expression. To work on non-filename-preserving storage systems, portable tool descriptions should avoid constructing new values from `location`, but should construct relative references using `basename` or `nameroot` instead. If a value in `secondaryFiles` is a string that is not an expression, it specifies that the following pattern should be applied to the path of the primary file to yield a filename relative to the primary File: 1. If string ends with `?` character, remove the last `?` and mark the resulting secondary file as optional. 2. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 3. Append the remainder of the string to the end of the file path. streamable: description: |- Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. type: boolean type: anyOf: - $ref: '#/definitions/CommandOutputArraySchema' - $ref: '#/definitions/CommandOutputRecordSchema' - $ref: '#/definitions/CommandOutputEnumSchema' - items: anyOf: - $ref: '#/definitions/CommandOutputArraySchema' - $ref: '#/definitions/CommandOutputRecordSchema' - $ref: '#/definitions/CommandOutputEnumSchema' - type: string type: array - type: string description: Specify valid types of data that may be assigned to this parameter. required: - type type: object CommandOutputRecordField: description: Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordField oneOf: - additionalProperties: false properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. format: description: |- Only valid when `type: File` or is an array of `items: File`. This is the file format that will be assigned to the output File object. type: string label: description: A short, human-readable label of this object. type: string name: description: The name of the field type: string outputBinding: $ref: '#/definitions/CommandOutputBinding' description: |- Describes how to generate this output object based on the files produced by a CommandLineTool secondaryFiles: anyOf: - $ref: '#/definitions/SecondaryFileSchema' - items: $ref: '#/definitions/SecondaryFileSchema' type: array description: |- Only valid when `type: File` or is an array of `items: File`. Provides a pattern or expression specifying files or directories that should be included alongside the primary file. Secondary files may be required or optional. When not explicitly specified, secondary files specified for `inputs` are required and `outputs` are optional. An implementation must include matching Files and Directories in the `secondaryFiles` property of the primary file. These Files and Directories must be transferred and staged alongside the primary file. An implementation may fail workflow execution if a required secondary file does not exist. If the value is an expression, the value of `self` in the expression must be the primary input or output File object to which this binding applies. The `basename`, `nameroot` and `nameext` fields must be present in `self`. For `CommandLineTool` outputs the `path` field must also be present. The expression must return a filename string relative to the path to the primary File, a File or Directory object with either `path` or `location` and `basename` fields set, or an array consisting of strings or File or Directory objects. It is legal to reference an unchanged File or Directory object taken from input as a secondaryFile. The expression may return "null" in which case there is no secondaryFile from that expression. To work on non-filename-preserving storage systems, portable tool descriptions should avoid constructing new values from `location`, but should construct relative references using `basename` or `nameroot` instead. If a value in `secondaryFiles` is a string that is not an expression, it specifies that the following pattern should be applied to the path of the primary file to yield a filename relative to the primary File: 1. If string ends with `?` character, remove the last `?` and mark the resulting secondary file as optional. 2. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 3. Append the remainder of the string to the end of the file path. streamable: description: |- Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. type: boolean type: anyOf: - $ref: '#/definitions/CommandOutputArraySchema' - $ref: '#/definitions/CommandOutputRecordSchema' - $ref: '#/definitions/CommandOutputEnumSchema' - items: anyOf: - $ref: '#/definitions/CommandOutputArraySchema' - $ref: '#/definitions/CommandOutputRecordSchema' - $ref: '#/definitions/CommandOutputEnumSchema' - type: string type: array - type: string description: The field type required: - name - type type: object - type: array items: anyOf: - $ref: '#/definitions/CommandOutputArraySchema' - $ref: '#/definitions/CommandOutputRecordSchema' - $ref: '#/definitions/CommandOutputEnumSchema' - items: anyOf: - $ref: '#/definitions/CommandOutputArraySchema' - $ref: '#/definitions/CommandOutputRecordSchema' - $ref: '#/definitions/CommandOutputEnumSchema' - type: string type: array - type: string description: The field type CommandOutputRecordSchema: additionalProperties: false description: Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordSchema properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. fields: description: Defines the fields of the record. oneOf: - items: $ref: '#/definitions/CommandOutputRecordField' type: array - patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: $ref: '#/definitions/CommandOutputRecordFieldMap' type: object label: description: A short, human-readable label of this object. type: string name: description: The identifier for this type type: string type: const: record description: Must be `record` type: string required: - type type: object DefaultFetcher: additionalProperties: false type: object Dictionary: additionalProperties: $ref: '#/definitions/T' type: object Dictionary: additionalProperties: $ref: '#/definitions/T' type: object Directory: additionalProperties: false description: |- Represents a directory to present to a command line tool. Directories are represented as objects with `class` of `Directory`. Directory objects have a number of properties that provide metadata about the directory. The `location` property of a Directory is a IRI that uniquely identifies the directory. Implementations must support the file:// IRI scheme and may support other schemes such as http://. Alternately to `location`, implementations must also accept the `path` property on Directory, which must be a filesystem path available on the same host as the CWL runner (for inputs) or the runtime environment of a command line tool execution (for command line tool outputs). A Directory object may have a `listing` field. This is a list of File and Directory objects that are contained in the Directory. For each entry in `listing`, the `basename` property defines the name of the File or Subdirectory when staged to disk. If `listing` is not provided, the implementation must have some way of fetching the Directory listing at runtime based on the `location` field. If a Directory does not have `location`, it is a Directory literal. A Directory literal must provide `listing`. Directory literals must be created on disk at runtime as needed. The resources in a Directory literal do not need to have any implied relationship in their `location`. For example, a Directory listing may contain two files located on different hosts. It is the responsibility of the runtime to ensure that those files are staged to disk appropriately. Secondary files associated with files in `listing` must also be staged to the same Directory. When executing a CommandLineTool, Directories must be recursively staged first and have local values of `path` assigned. Directory objects in CommandLineTool output must provide either a `location` IRI or a `path` property in the context of the tool execution runtime (local to the compute node, or within the executing container). An ExpressionTool may forward file references from input to output by using the same value for `location`. Name conflicts (the same `basename` appearing multiple times in `listing` or in any entry in `secondaryFiles` in the listing) is a fatal error. properties: basename: description: |- The base name of the directory, that is, the name of the file without any leading directory path. The base name must not contain a slash `/`. If not provided, the implementation must set this field based on the `location` field by taking the final path component after parsing `location` as an IRI. If `basename` is provided, it is not required to match the value from `location`. When this file is made available to a CommandLineTool, it must be named with `basename`, i.e. the final component of the `path` field must match `basename`. type: string class: const: Directory description: Must be `Directory` to indicate this object describes a Directory. type: string listing: description: |- List of files or subdirectories contained in this directory. The name of each file or subdirectory is determined by the `basename` field of each `File` or `Directory` object. It is an error if a `File` shares a `basename` with any other entry in `listing`. If two or more `Directory` object share the same `basename`, this must be treated as equivalent to a single subdirectory with the listings recursively merged. items: anyOf: - $ref: '#/definitions/Directory' - $ref: '#/definitions/File' type: array location: description: |- An IRI that identifies the directory resource. This may be a relative reference, in which case it must be resolved using the base IRI of the document. The location may refer to a local or remote resource. If the `listing` field is not set, the implementation must use the location IRI to retrieve directory listing. If an implementation is unable to retrieve the directory listing stored at a remote resource (due to unsupported protocol, access denied, or other issue) it must signal an error. If the `location` field is not provided, the `listing` field must be provided. The implementation must assign a unique identifier for the `location` field. If the `path` field is provided but the `location` field is not, an implementation may assign the value of the `path` field to `location`, then follow the rules above. type: string path: description: |- The local path where the Directory is made available prior to executing a CommandLineTool. This must be set by the implementation. This field must not be used in any other context. The command line tool being executed must be able to access the directory at `path` using the POSIX `opendir(2)` syscall. If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, ``, ``, and ``) or characters [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) then implementations may terminate the process with a `permanentFailure`. type: string required: - class type: object Dirent: additionalProperties: false description: |- Define a file or subdirectory that must be staged to a particular place prior to executing the command line tool. May be the result of executing an expression, such as building a configuration file from a template. Usually files are staged within the [designated output directory](#Runtime_environment). However, under certain circumstances, files may be staged at arbitrary locations, see discussion for `entryname`. properties: entry: description: |- If the value is a string literal or an expression which evaluates to a string, a new text file must be created with the string as the file contents. If the value is an expression that evaluates to a `File` or `Directory` object, or an array of `File` or `Directory` objects, this indicates the referenced file or directory should be added to the designated output directory prior to executing the tool. If the value is an expression that evaluates to `null`, nothing is added to the designated output directory, the entry has no effect. If the value is an expression that evaluates to some other array, number, or object not consisting of `File` or `Directory` objects, a new file must be created with the value serialized to JSON text as the file contents. The JSON serialization behavior should match the behavior of string interpolation of [Parameter references](#Parameter_references). type: string entryname: description: |- The "target" name of the file or subdirectory. If `entry` is a File or Directory, the `entryname` field overrides the value of `basename` of the File or Directory object. * Required when `entry` evaluates to file contents only * Optional when `entry` evaluates to a File or Directory object with a `basename` * Invalid when `entry` evaluates to an array of File or Directory objects. If `entryname` is a relative path, it specifies a name within the designated output directory. A relative path starting with `../` or that resolves to location above the designated output directory is an error. If `entryname` is an absolute path (starts with a slash `/`) it is an error unless the following conditions are met: * `DockerRequirement` is present in `requirements` * The program is will run inside a software container where, from the perspective of the program, the root filesystem is not shared with any other user or running program. In this case, and the above conditions are met, then `entryname` may specify the absolute path within the container where the file or directory must be placed. type: string writable: description: |- If true, the File or Directory (or array of Files or Directories) declared in `entry` must be writable by the tool. Changes to the file or directory must be isolated and not visible by any other CommandLineTool process. This may be implemented by making a copy of the original file or directory. Disruptive changes to the referenced file or directory must not be allowed unless `InplaceUpdateRequirement.inplaceUpdate` is true. Default false (files and directories read-only by default). A directory marked as `writable: true` implies that all files and subdirectories are recursively writable as well. If `writable` is false, the file may be made available using a bind mount or file system link to avoid unnecessary copying of the input file. Command line tools may receive an error on attempting to rename or delete files or directories that are not explicitly marked as writable. type: boolean required: - entry type: object DockerRequirement: additionalProperties: false description: |- Indicates that a workflow component should be run in a [Docker](https://docker.com) or Docker-compatible (such as [Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment and specifies how to fetch or build the image. If a CommandLineTool lists `DockerRequirement` under `hints` (or `requirements`), it may (or must) be run in the specified Docker container. The platform must first acquire or install the correct Docker image as specified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`. The platform must execute the tool in the container using `docker run` with the appropriate Docker image and tool command line. The workflow platform may provide input files and the designated output directory through the use of volume bind mounts. The platform should rewrite file paths in the input object to correspond to the Docker bind mounted locations. That is, the platform should rewrite values in the parameter context such as `runtime.outdir`, `runtime.tmpdir` and others to be valid paths within the container. The platform must ensure that `runtime.outdir` and `runtime.tmpdir` are distinct directories. When running a tool contained in Docker, the workflow platform must not assume anything about the contents of the Docker container, such as the presence or absence of specific software, except to assume that the generated command line represents a valid command within the runtime environment of the container. A container image may specify an [ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint) and/or [CMD](https://docs.docker.com/engine/reference/builder/#cmd). Command line arguments will be appended after all elements of ENTRYPOINT, and will override all elements specified using CMD (in other words, CMD is only used when the CommandLineTool definition produces an empty command line). Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility concerns of the implicit hidden execution point (For further discussion, see [https://doi.org/10.12688/f1000research.15140.1](https://doi.org/10.12688/f1000research.15140.1)). Portable CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD. CommandLineTools which do rely on ENTRYPOINT or CMD must list `DockerRequirement` in the `requirements` section. ## Interaction with other requirements If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a DockerRequirement, the environment variables must be provided to Docker using `--env` or `--env-file` and interact with the container's preexisting environment as defined by Docker. properties: class: const: DockerRequirement description: Always 'DockerRequirement' type: string dockerFile: description: Supply the contents of a Dockerfile which will be built using `docker build`. type: string dockerImageId: description: |- The image id that will be used for `docker run`. May be a human-readable image name or the image identifier hash. May be skipped if `dockerPull` is specified, in which case the `dockerPull` image id must be used. type: string dockerImport: description: Provide HTTP URL to download and gunzip a Docker images using `docker import. type: string dockerLoad: description: Specify an HTTP URL from which to download a Docker image using `docker load`. type: string dockerOutputDirectory: description: |- Set the designated output directory to a specific location inside the Docker container. type: string dockerPull: description: |- Specify a Docker image to retrieve using `docker pull`. Can contain the immutable digest to ensure an exact container is used: `dockerPull: ubuntu@sha256:45b23dee08af5e43a7fea6c4cf9c25ccf269ee113168c19722f87876677c5cb2` type: string required: - class type: object EnvVarRequirement: additionalProperties: false description: |- Define a list of environment variables which will be set in the execution environment of the tool. See `EnvironmentDef` for details. properties: class: const: EnvVarRequirement description: Always 'EnvVarRequirement' type: string envDef: description: The list of environment variables. oneOf: - items: anyOf: - $ref: '#/definitions/EnvironmentDef' - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' type: array - patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: type: string required: - class - envDef type: object EnvironmentDef: additionalProperties: false description: |- Define an environment variable that will be set in the runtime environment by the workflow platform when executing the command line tool. May be the result of executing an expression, such as getting a parameter from input. properties: envName: description: The environment variable name type: string envValue: description: The environment variable value type: string required: - envName - envValue type: object ExpressionTool: description: |- 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. properties: class: const: ExpressionTool type: string cwlVersion: description: |- CWL document version. Always required at the document root. Not required for a Process embedded inside another Process. enum: - draft-2 - draft-3 - draft-3.dev1 - draft-3.dev2 - draft-3.dev3 - draft-3.dev4 - draft-3.dev5 - draft-4.dev1 - draft-4.dev2 - draft-4.dev3 - v1.0 - v1.0.dev4 - v1.1 - v1.1.0-dev1 - v1.2 - v1.2.0-dev1 - v1.2.0-dev2 - v1.2.0-dev3 - v1.2.0-dev4 - v1.2.0-dev5 type: string doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. expression: description: |- The expression to execute. The expression must return a plain Javascript object which matches the output parameters of the ExpressionTool. type: string hints: description: |- Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. 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. oneOf: - items: anyOf: - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' - $ref: '#/definitions/InlineJavascriptRequirement' - $ref: '#/definitions/SchemaDefRequirement' - $ref: '#/definitions/LoadListingRequirement' - $ref: '#/definitions/DockerRequirement' - $ref: '#/definitions/SoftwareRequirement' - $ref: '#/definitions/InitialWorkDirRequirement' - $ref: '#/definitions/EnvVarRequirement' - $ref: '#/definitions/ShellCommandRequirement' - $ref: '#/definitions/ResourceRequirement' - $ref: '#/definitions/WorkReuse' - $ref: '#/definitions/NetworkAccess' - $ref: '#/definitions/InplaceUpdateRequirement' - $ref: '#/definitions/ToolTimeLimit' - $ref: '#/definitions/SubworkflowFeatureRequirement' - $ref: '#/definitions/ScatterFeatureRequirement' - $ref: '#/definitions/MultipleInputFeatureRequirement' - $ref: '#/definitions/StepInputExpressionRequirement' type: array - type: object properties: InlineJavascriptRequirement: anyOf: - $ref: '#/definitions/InlineJavascriptRequirementMap' - type: object properties: {} additionalProperties: false SchemaDefRequirement: anyOf: - $ref: '#/definitions/SchemaDefRequirementMap' - type: object properties: {} additionalProperties: false LoadListingRequirement: anyOf: - $ref: '#/definitions/LoadListingRequirementMap' - type: object properties: {} additionalProperties: false DockerRequirement: anyOf: - $ref: '#/definitions/DockerRequirementMap' - type: object properties: {} additionalProperties: false SoftwareRequirement: anyOf: - $ref: '#/definitions/SoftwareRequirementMap' - type: object properties: {} additionalProperties: false InitialWorkDirRequirement: anyOf: - $ref: '#/definitions/InitialWorkDirRequirementMap' - type: object properties: {} additionalProperties: false EnvVarRequirement: anyOf: - $ref: '#/definitions/EnvVarRequirementMap' - type: object properties: {} additionalProperties: false ShellCommandRequirement: anyOf: - $ref: '#/definitions/ShellCommandRequirementMap' - type: object properties: {} additionalProperties: false ResourceRequirement: anyOf: - $ref: '#/definitions/ResourceRequirementMap' - type: object properties: {} additionalProperties: false WorkReuse: anyOf: - $ref: '#/definitions/WorkReuseMap' - type: object properties: {} additionalProperties: false NetworkAccess: anyOf: - $ref: '#/definitions/NetworkAccessMap' - type: object properties: {} additionalProperties: false InplaceUpdateRequirement: anyOf: - $ref: '#/definitions/InplaceUpdateRequirementMap' - type: object properties: {} additionalProperties: false ToolTimeLimit: anyOf: - $ref: '#/definitions/ToolTimeLimitMap' - type: object properties: {} additionalProperties: false SubworkflowFeatureRequirement: anyOf: - $ref: '#/definitions/SubworkflowFeatureRequirementMap' - type: object properties: {} additionalProperties: false ScatterFeatureRequirement: anyOf: - $ref: '#/definitions/ScatterFeatureRequirementMap' - type: object properties: {} additionalProperties: false MultipleInputFeatureRequirement: anyOf: - $ref: '#/definitions/MultipleInputFeatureRequirementMap' - type: object properties: {} additionalProperties: false StepInputExpressionRequirement: anyOf: - $ref: '#/definitions/StepInputExpressionRequirementMap' - type: object properties: {} additionalProperties: false additionalProperties: false id: description: |- The unique identifier for this object. Only useful for `$graph` at `Process` level. Should not be exposed to users in graphical or terminal user interfaces. type: string inputs: description: |- Defines the input parameters of the process. 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 to build a user interface for constructing the input object. When accepting an input object, all input parameters must have a value. If an input parameter is missing from the input object, it must be assigned a value of `null` (or the value of `default` for that parameter, if provided) for the purposes of validation and evaluation of expressions. oneOf: - items: $ref: '#/definitions/WorkflowInputParameter' type: array - patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: oneOf: - $ref: '#/definitions/WorkflowInputParameter' - anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - items: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - type: string type: array - type: string description: Specify valid types of data that may be assigned to this parameter. - type: array items: oneOf: - type: string - $ref: '#/definitions/WorkflowInputParameter' type: object intent: description: |- An identifier for the type of computational operation, of this Process. Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for [`CommandLineTool`](CommandLineTool.html#CommandLineTool), [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool). If provided, then this must be an IRI of a concept node that represents the type of operation, preferably defined within an ontology. For example, in the domain of bioinformatics, one can use an IRI from the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), like [Alignment](http://edamontology.org/operation_2928), or [Clustering](http://edamontology.org/operation_3432); or a more specific Operation concept like [Split read mapping](http://edamontology.org/operation_3199). items: type: string type: array label: description: A short, human-readable label of this object. type: string outputs: description: |- Defines the parameters representing the output of the process. May be used to generate and/or validate the output object. oneOf: - items: $ref: '#/definitions/ExpressionToolOutputParameter' type: array - patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: oneOf: - $ref: '#/definitions/ExpressionToolOutputParameter' - anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - items: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - type: string type: array - type: string description: |- Specify valid types of data that may be assigned to this parameter. Note that this field just acts as a hint, as the outputs of an ExpressionTool process are always considered valid. - type: array items: oneOf: - type: string - $ref: '#/definitions/ExpressionToolOutputParameter' type: object requirements: description: |- Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. 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. oneOf: - items: anyOf: - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' - $ref: '#/definitions/InlineJavascriptRequirement' - $ref: '#/definitions/SchemaDefRequirement' - $ref: '#/definitions/LoadListingRequirement' - $ref: '#/definitions/DockerRequirement' - $ref: '#/definitions/SoftwareRequirement' - $ref: '#/definitions/InitialWorkDirRequirement' - $ref: '#/definitions/EnvVarRequirement' - $ref: '#/definitions/ShellCommandRequirement' - $ref: '#/definitions/ResourceRequirement' - $ref: '#/definitions/WorkReuse' - $ref: '#/definitions/NetworkAccess' - $ref: '#/definitions/InplaceUpdateRequirement' - $ref: '#/definitions/ToolTimeLimit' - $ref: '#/definitions/SubworkflowFeatureRequirement' - $ref: '#/definitions/ScatterFeatureRequirement' - $ref: '#/definitions/MultipleInputFeatureRequirement' - $ref: '#/definitions/StepInputExpressionRequirement' type: array - type: object properties: InlineJavascriptRequirement: anyOf: - $ref: '#/definitions/InlineJavascriptRequirementMap' - type: object properties: {} additionalProperties: false SchemaDefRequirement: anyOf: - $ref: '#/definitions/SchemaDefRequirementMap' - type: object properties: {} additionalProperties: false LoadListingRequirement: anyOf: - $ref: '#/definitions/LoadListingRequirementMap' - type: object properties: {} additionalProperties: false DockerRequirement: anyOf: - $ref: '#/definitions/DockerRequirementMap' - type: object properties: {} additionalProperties: false SoftwareRequirement: anyOf: - $ref: '#/definitions/SoftwareRequirementMap' - type: object properties: {} additionalProperties: false InitialWorkDirRequirement: anyOf: - $ref: '#/definitions/InitialWorkDirRequirementMap' - type: object properties: {} additionalProperties: false EnvVarRequirement: anyOf: - $ref: '#/definitions/EnvVarRequirementMap' - type: object properties: {} additionalProperties: false ShellCommandRequirement: anyOf: - $ref: '#/definitions/ShellCommandRequirementMap' - type: object properties: {} additionalProperties: false ResourceRequirement: anyOf: - $ref: '#/definitions/ResourceRequirementMap' - type: object properties: {} additionalProperties: false WorkReuse: anyOf: - $ref: '#/definitions/WorkReuseMap' - type: object properties: {} additionalProperties: false NetworkAccess: anyOf: - $ref: '#/definitions/NetworkAccessMap' - type: object properties: {} additionalProperties: false InplaceUpdateRequirement: anyOf: - $ref: '#/definitions/InplaceUpdateRequirementMap' - type: object properties: {} additionalProperties: false ToolTimeLimit: anyOf: - $ref: '#/definitions/ToolTimeLimitMap' - type: object properties: {} additionalProperties: false SubworkflowFeatureRequirement: anyOf: - $ref: '#/definitions/SubworkflowFeatureRequirementMap' - type: object properties: {} additionalProperties: false ScatterFeatureRequirement: anyOf: - $ref: '#/definitions/ScatterFeatureRequirementMap' - type: object properties: {} additionalProperties: false MultipleInputFeatureRequirement: anyOf: - $ref: '#/definitions/MultipleInputFeatureRequirementMap' - type: object properties: {} additionalProperties: false StepInputExpressionRequirement: anyOf: - $ref: '#/definitions/StepInputExpressionRequirementMap' - type: object properties: {} additionalProperties: false additionalProperties: false required: - class - expression - inputs - outputs type: object ExpressionToolOutputParameter: additionalProperties: false description: Auto-generated class implementation for https://w3id.org/cwl/cwl#ExpressionToolOutputParameter properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. format: description: |- Only valid when `type: File` or is an array of `items: File`. This is the file format that will be assigned to the output File object. type: string id: description: The unique identifier for this object. type: string label: description: A short, human-readable label of this object. type: string secondaryFiles: anyOf: - $ref: '#/definitions/SecondaryFileSchema' - items: $ref: '#/definitions/SecondaryFileSchema' type: array description: |- Only valid when `type: File` or is an array of `items: File`. Provides a pattern or expression specifying files or directories that should be included alongside the primary file. Secondary files may be required or optional. When not explicitly specified, secondary files specified for `inputs` are required and `outputs` are optional. An implementation must include matching Files and Directories in the `secondaryFiles` property of the primary file. These Files and Directories must be transferred and staged alongside the primary file. An implementation may fail workflow execution if a required secondary file does not exist. If the value is an expression, the value of `self` in the expression must be the primary input or output File object to which this binding applies. The `basename`, `nameroot` and `nameext` fields must be present in `self`. For `CommandLineTool` outputs the `path` field must also be present. The expression must return a filename string relative to the path to the primary File, a File or Directory object with either `path` or `location` and `basename` fields set, or an array consisting of strings or File or Directory objects. It is legal to reference an unchanged File or Directory object taken from input as a secondaryFile. The expression may return "null" in which case there is no secondaryFile from that expression. To work on non-filename-preserving storage systems, portable tool descriptions should avoid constructing new values from `location`, but should construct relative references using `basename` or `nameroot` instead. If a value in `secondaryFiles` is a string that is not an expression, it specifies that the following pattern should be applied to the path of the primary file to yield a filename relative to the primary File: 1. If string ends with `?` character, remove the last `?` and mark the resulting secondary file as optional. 2. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 3. Append the remainder of the string to the end of the file path. streamable: description: |- Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. type: boolean type: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - items: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - type: string type: array - type: string description: |- Specify valid types of data that may be assigned to this parameter. Note that this field just acts as a hint, as the outputs of an ExpressionTool process are always considered valid. required: - type type: object Fetcher: oneOf: - $ref: '#/definitions/DefaultFetcher' File: additionalProperties: false description: |- Represents a file (or group of files when `secondaryFiles` is provided) that will be accessible by tools using standard POSIX file system call API such as open(2) and read(2). Files are represented as objects with `class` of `File`. File objects have a number of properties that provide metadata about the file. The `location` property of a File is a IRI that uniquely identifies the file. Implementations must support the `file://` IRI scheme and may support other schemes such as `http://` and `https://`. The value of `location` may also be a relative reference, in which case it must be resolved relative to the IRI of the document it appears in. Alternately to `location`, implementations must also accept the `path` property on File, which must be a filesystem path available on the same host as the CWL runner (for inputs) or the runtime environment of a command line tool execution (for command line tool outputs). If no `location` or `path` is specified, a file object must specify `contents` with the UTF-8 text content of the file. This is a "file literal". File literals do not correspond to external resources, but are created on disk with `contents` with when needed for executing a tool. Where appropriate, expressions can return file literals to define new files on a runtime. The maximum size of `contents` is 64 kilobytes. The `basename` property defines the filename on disk where the file is staged. This may differ from the resource name. If not provided, `basename` must be computed from the last path part of `location` and made available to expressions. The `secondaryFiles` property is a list of File or Directory objects that must be staged in the same directory as the primary file. It is an error for file names to be duplicated in `secondaryFiles`. The `size` property is the size in bytes of the File. It must be computed from the resource and made available to expressions. The `checksum` field contains a cryptographic hash of the file content for use it verifying file contents. Implementations may, at user option, enable or disable computation of the `checksum` field for performance or other reasons. However, the ability to compute output checksums is required to pass the CWL conformance test suite. When executing a CommandLineTool, the files and secondary files may be staged to an arbitrary directory, but must use the value of `basename` for the filename. The `path` property must be file path in the context of the tool execution runtime (local to the compute node, or within the executing container). All computed properties should be available to expressions. File literals also must be staged and `path` must be set. When collecting CommandLineTool outputs, `glob` matching returns file paths (with the `path` property) and the derived properties. This can all be modified by `outputEval`. Alternately, if the file `cwl.output.json` is present in the output, `outputBinding` is ignored. File objects in the output must provide either a `location` IRI or a `path` property in the context of the tool execution runtime (local to the compute node, or within the executing container). When evaluating an ExpressionTool, file objects must be referenced via `location` (the expression tool does not have access to files on disk so `path` is meaningless) or as file literals. It is legal to return a file object with an existing `location` but a different `basename`. The `loadContents` field of ExpressionTool inputs behaves the same as on CommandLineTool inputs, however it is not meaningful on the outputs. An ExpressionTool may forward file references from input to output by using the same value for `location`. properties: basename: description: |- The base name of the file, that is, the name of the file without any leading directory path. The base name must not contain a slash `/`. If not provided, the implementation must set this field based on the `location` field by taking the final path component after parsing `location` as an IRI. If `basename` is provided, it is not required to match the value from `location`. When this file is made available to a CommandLineTool, it must be named with `basename`, i.e. the final component of the `path` field must match `basename`. type: string checksum: description: |- Optional hash code for validating file integrity. Currently, must be in the form "sha1$ + hexadecimal string" using the SHA-1 algorithm. type: string class: const: File description: Must be `File` to indicate this object describes a file. type: string contents: description: |- File contents literal. If neither `location` nor `path` is provided, `contents` must be non-null. The implementation must assign a unique identifier for the `location` field. When the file is staged as input to CommandLineTool, the value of `contents` must be written to a file. If `contents` is set as a result of a Javascript expression, an `entry` in `InitialWorkDirRequirement`, or read in from `cwl.output.json`, there is no specified upper limit on the size of `contents`. Implementations may have practical limits on the size of `contents` based on memory and storage available to the workflow runner or other factors. If the `loadContents` field of an `InputParameter` or `OutputParameter` is true, and the input or output File object `location` is valid, the file must be a UTF-8 text file 64 KiB or smaller, and the implementation must read the entire contents of the file and place it in the `contents` field. If the size of the file is greater than 64 KiB, the implementation must raise a fatal error. type: string dirname: description: |- The name of the directory containing file, that is, the path leading up to the final slash in the path such that `dirname + '/' + basename == path`. The implementation must set this field based on the value of `path` prior to evaluating parameter references or expressions in a CommandLineTool document. This field must not be used in any other context. type: string format: description: |- The format of the file: this must be an IRI of a concept node that represents the file format, preferably defined within an ontology. If no ontology is available, file formats may be tested by exact match. Reasoning about format compatibility must be done by checking that an input file format is the same, `owl:equivalentClass` or `rdfs:subClassOf` the format required by the input parameter. `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if ` owl:equivalentClass ` and ` owl:subclassOf ` then infer ` owl:subclassOf `. File format ontologies may be provided in the "$schemas" metadata at the root of the document. If no ontologies are specified in `$schemas`, the runtime may perform exact file format matches. type: string location: description: |- An IRI that identifies the file resource. This may be a relative reference, in which case it must be resolved using the base IRI of the document. The location may refer to a local or remote resource; the implementation must use the IRI to retrieve file content. If an implementation is unable to retrieve the file content stored at a remote resource (due to unsupported protocol, access denied, or other issue) it must signal an error. If the `location` field is not provided, the `contents` field must be provided. The implementation must assign a unique identifier for the `location` field. If the `path` field is provided but the `location` field is not, an implementation may assign the value of the `path` field to `location`, then follow the rules above. type: string nameext: description: |- The basename extension such that `nameroot + nameext == basename`, and `nameext` is empty or begins with a period and contains at most one period. Leading periods on the basename are ignored; a basename of `.cshrc` will have an empty `nameext`. The implementation must set this field automatically based on the value of `basename` prior to evaluating parameter references or expressions. type: string nameroot: description: |- The basename root such that `nameroot + nameext == basename`, and `nameext` is empty or begins with a period and contains at most one period. For the purposes of path splitting leading periods on the basename are ignored; a basename of `.cshrc` will have a nameroot of `.cshrc`. The implementation must set this field automatically based on the value of `basename` prior to evaluating parameter references or expressions. type: string path: description: |- The local host path where the File is available when a CommandLineTool is executed. This field must be set by the implementation. The final path component must match the value of `basename`. This field must not be used in any other context. The command line tool being executed must be able to access the file at `path` using the POSIX `open(2)` syscall. As a special case, if the `path` field is provided but the `location` field is not, an implementation may assign the value of the `path` field to `location`, and remove the `path` field. If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, ``, ``, and ``) or characters [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) then implementations may terminate the process with a `permanentFailure`. type: string secondaryFiles: description: |- A list of additional files or directories that are associated with the primary file and must be transferred alongside the primary file. Examples include indexes of the primary file, or external references which must be included when loading primary document. A file object listed in `secondaryFiles` may itself include `secondaryFiles` for which the same rules apply. items: anyOf: - $ref: '#/definitions/Directory' - $ref: '#/definitions/File' type: array size: description: Optional file size (in bytes) type: number required: - class type: object InitialWorkDirRequirement: additionalProperties: false description: |- Define a list of files and subdirectories that must be staged by the workflow platform prior to executing the command line tool. Normally files are staged within the designated output directory. However, when running inside containers, files may be staged at arbitrary locations, see discussion for [`Dirent.entryname`](#Dirent). Together with `DockerRequirement.dockerOutputDirectory` it is possible to control the locations of both input and output files when running in containers. properties: class: const: InitialWorkDirRequirement description: InitialWorkDirRequirement type: string listing: anyOf: - items: anyOf: - anyOf: - $ref: '#/definitions/Directory' - $ref: '#/definitions/File' - items: anyOf: - anyOf: - $ref: '#/definitions/Directory' - $ref: '#/definitions/File' - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' type: array - $ref: '#/definitions/Dirent' - type: string - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' type: array - type: string description: |- The list of files or subdirectories that must be staged prior to executing the command line tool. Return type of each expression must validate as `["null", File, Directory, Dirent, {type: array, items: [File, Directory]}]`. Each `File` or `Directory` that is returned by an Expression must be added to the designated output directory prior to executing the tool. Each `Dirent` record that is listed or returned by an expression specifies a file to be created or staged in the designated output directory prior to executing the tool. Expressions may return null, in which case they have no effect. Files or Directories which are listed in the input parameters and appear in the `InitialWorkDirRequirement` listing must have their `path` set to their staged location. If the same File or Directory appears more than once in the `InitialWorkDirRequirement` listing, the implementation must choose exactly one value for `path`; how this value is chosen is undefined. required: - class type: object InlineJavascriptRequirement: additionalProperties: false description: |- Indicates that the workflow platform must support inline Javascript expressions. If this requirement is not present, the workflow platform must not perform expression interpolation. properties: class: const: InlineJavascriptRequirement description: Always 'InlineJavascriptRequirement' type: string expressionLib: description: |- Additional code fragments that will also be inserted before executing the expression code. Allows for function definitions that may be called from CWL expressions. items: anyOf: - type: string - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' type: array required: - class type: object InplaceUpdateRequirement: additionalProperties: false description: |2- If `inplaceUpdate` is true, then an implementation supporting this feature may permit tools to directly update files with `writable: true` in InitialWorkDirRequirement. That is, as an optimization, files may be destructively modified in place as opposed to copied and updated. An implementation must ensure that only one workflow step may access a writable file at a time. It is an error if a file which is writable by one workflow step file is accessed (for reading or writing) by any other workflow step running independently. However, a file which has been updated in a previous completed step may be used as input to multiple steps, provided it is read-only in every step. Workflow steps which modify a file must produce the modified file as output. Downstream steps which further process the file must use the output of previous steps, and not refer to a common input (this is necessary for both ordering and correctness). Workflow authors should provide this in the `hints` section. The intent of this feature is that workflows produce the same results whether or not InplaceUpdateRequirement is supported by the implementation, and this feature is primarily available as an optimization for particular environments. Users and implementers should be aware that workflows that destructively modify inputs may not be repeatable or reproducible. In particular, enabling this feature implies that WorkReuse should not be enabled. properties: class: const: InplaceUpdateRequirement description: Always 'InplaceUpdateRequirement' type: string inplaceUpdate: type: boolean required: - class - inplaceUpdate type: object InputArraySchema: additionalProperties: false description: Auto-generated class implementation for https://w3id.org/cwl/cwl#InputArraySchema properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. items: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - items: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - type: string type: array - type: string description: Defines the type of the array elements. label: description: A short, human-readable label of this object. type: string name: description: The identifier for this type type: string type: const: array description: Must be `array` type: string required: - items - type type: object InputBinding: additionalProperties: false description: Auto-generated class implementation for https://w3id.org/cwl/cwl#InputBinding properties: loadContents: description: |- Use of `loadContents` in `InputBinding` is deprecated. Preserved for v1.0 backwards compatibility. Will be removed in CWL v2.0. Use `InputParameter.loadContents` instead. type: boolean required: [] type: object InputEnumSchema: additionalProperties: false description: Auto-generated class implementation for https://w3id.org/cwl/cwl#InputEnumSchema properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. label: description: A short, human-readable label of this object. type: string name: description: The identifier for this type type: string symbols: description: Defines the set of valid symbols. items: type: string type: array type: const: enum description: Must be `enum` type: string required: - symbols - type type: object InputRecordField: description: Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordField oneOf: - additionalProperties: false properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. format: anyOf: - items: type: string type: array - type: string description: |- Only valid when `type: File` or is an array of `items: File`. This must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferably defined within an ontology. If no ontology is available, file formats may be tested by exact match. label: description: A short, human-readable label of this object. type: string loadContents: description: |- Only valid when `type: File` or is an array of `items: File`. If true, the file (or each file in the array) must be a UTF-8 text file 64 KiB or smaller, and the implementation must read the entire contents of the file (or file array) and place it in the `contents` field of the File object for use by expressions. If the size of the file is greater than 64 KiB, the implementation must raise a fatal error. type: boolean loadListing: description: |- Only valid when `type: Directory` or is an array of `items: Directory`. Specify the desired behavior for loading the `listing` field of a Directory object for use by expressions. The order of precedence for loadListing is: 1. `loadListing` on an individual parameter 2. Inherited from `LoadListingRequirement` 3. By default: `no_listing` enum: - deep_listing - no_listing - shallow_listing type: string name: description: The name of the field type: string secondaryFiles: anyOf: - $ref: '#/definitions/SecondaryFileSchema' - items: $ref: '#/definitions/SecondaryFileSchema' type: array description: |- Only valid when `type: File` or is an array of `items: File`. Provides a pattern or expression specifying files or directories that should be included alongside the primary file. Secondary files may be required or optional. When not explicitly specified, secondary files specified for `inputs` are required and `outputs` are optional. An implementation must include matching Files and Directories in the `secondaryFiles` property of the primary file. These Files and Directories must be transferred and staged alongside the primary file. An implementation may fail workflow execution if a required secondary file does not exist. If the value is an expression, the value of `self` in the expression must be the primary input or output File object to which this binding applies. The `basename`, `nameroot` and `nameext` fields must be present in `self`. For `CommandLineTool` outputs the `path` field must also be present. The expression must return a filename string relative to the path to the primary File, a File or Directory object with either `path` or `location` and `basename` fields set, or an array consisting of strings or File or Directory objects. It is legal to reference an unchanged File or Directory object taken from input as a secondaryFile. The expression may return "null" in which case there is no secondaryFile from that expression. To work on non-filename-preserving storage systems, portable tool descriptions should avoid constructing new values from `location`, but should construct relative references using `basename` or `nameroot` instead. If a value in `secondaryFiles` is a string that is not an expression, it specifies that the following pattern should be applied to the path of the primary file to yield a filename relative to the primary File: 1. If string ends with `?` character, remove the last `?` and mark the resulting secondary file as optional. 2. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 3. Append the remainder of the string to the end of the file path. streamable: description: |- Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. type: boolean type: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - items: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - type: string type: array - type: string description: The field type required: - name - type type: object - type: array items: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - items: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - type: string type: array - type: string description: The field type InputRecordSchema: additionalProperties: false description: Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordSchema properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. fields: description: Defines the fields of the record. oneOf: - items: $ref: '#/definitions/InputRecordField' type: array - patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: $ref: '#/definitions/InputRecordFieldMap' type: object label: description: A short, human-readable label of this object. type: string name: description: The identifier for this type type: string type: const: record description: Must be `record` type: string required: - type type: object LoadListingRequirement: additionalProperties: false description: |- Specify the desired behavior for loading the `listing` field of a Directory object for use by expressions. properties: class: const: LoadListingRequirement description: Always 'LoadListingRequirement' type: string loadListing: enum: - deep_listing - no_listing - shallow_listing type: string required: - class type: object LoadingOptions: additionalProperties: false properties: container: type: string copyFrom: $ref: '#/definitions/LoadingOptions' fetcher: $ref: '#/definitions/Fetcher' fileUri: type: string idx: $ref: '#/definitions/Dictionary' namespaces: $ref: '#/definitions/Dictionary' noLinkCheck: type: boolean originalDoc: {} rvocab: $ref: '#/definitions/Dictionary' schemas: $ref: '#/definitions/Dictionary' vocab: $ref: '#/definitions/Dictionary' required: - fetcher - idx - originalDoc - rvocab - vocab type: object MultipleInputFeatureRequirement: additionalProperties: false description: |- Indicates that the workflow platform must support multiple inbound data links listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput). properties: class: const: MultipleInputFeatureRequirement description: Always 'MultipleInputFeatureRequirement' type: string required: - class type: object NetworkAccess: additionalProperties: false description: |- Indicate whether a process requires outgoing IPv4/IPv6 network access. Choice of IPv4 or IPv6 is implementation and site specific, correct tools must support both. If `networkAccess` is false or not specified, tools must not assume network access, except for localhost (the loopback device). If `networkAccess` is true, the tool must be able to make outgoing connections to network resources. Resources may be on a private subnet or the public Internet. However, implementations and sites may apply their own security policies to restrict what is accessible by the tool. Enabling network access does not imply a publicly routable IP address or the ability to accept inbound connections. properties: class: const: NetworkAccess description: Always 'NetworkAccess' type: string networkAccess: type: - string - boolean required: - class - networkAccess type: object Operation: additionalProperties: false description: |- This record describes an abstract operation. It is a potential step of a workflow that has not yet been bound to a concrete implementation. It specifies an input and output signature, but does not provide enough information to be executed. An implementation (or other tooling) may provide a means of binding an Operation to a concrete process (such as Workflow, CommandLineTool, or ExpressionTool) with a compatible signature. properties: class: const: Operation type: string cwlVersion: description: |- CWL document version. Always required at the document root. Not required for a Process embedded inside another Process. enum: - draft-2 - draft-3 - draft-3.dev1 - draft-3.dev2 - draft-3.dev3 - draft-3.dev4 - draft-3.dev5 - draft-4.dev1 - draft-4.dev2 - draft-4.dev3 - v1.0 - v1.0.dev4 - v1.1 - v1.1.0-dev1 - v1.2 - v1.2.0-dev1 - v1.2.0-dev2 - v1.2.0-dev3 - v1.2.0-dev4 - v1.2.0-dev5 type: string doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. hints: description: |- Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. 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. oneOf: - items: anyOf: - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' - $ref: '#/definitions/InlineJavascriptRequirement' - $ref: '#/definitions/SchemaDefRequirement' - $ref: '#/definitions/LoadListingRequirement' - $ref: '#/definitions/DockerRequirement' - $ref: '#/definitions/SoftwareRequirement' - $ref: '#/definitions/InitialWorkDirRequirement' - $ref: '#/definitions/EnvVarRequirement' - $ref: '#/definitions/ShellCommandRequirement' - $ref: '#/definitions/ResourceRequirement' - $ref: '#/definitions/WorkReuse' - $ref: '#/definitions/NetworkAccess' - $ref: '#/definitions/InplaceUpdateRequirement' - $ref: '#/definitions/ToolTimeLimit' - $ref: '#/definitions/SubworkflowFeatureRequirement' - $ref: '#/definitions/ScatterFeatureRequirement' - $ref: '#/definitions/MultipleInputFeatureRequirement' - $ref: '#/definitions/StepInputExpressionRequirement' type: array - type: object properties: InlineJavascriptRequirement: anyOf: - $ref: '#/definitions/InlineJavascriptRequirementMap' - type: object properties: {} additionalProperties: false SchemaDefRequirement: anyOf: - $ref: '#/definitions/SchemaDefRequirementMap' - type: object properties: {} additionalProperties: false LoadListingRequirement: anyOf: - $ref: '#/definitions/LoadListingRequirementMap' - type: object properties: {} additionalProperties: false DockerRequirement: anyOf: - $ref: '#/definitions/DockerRequirementMap' - type: object properties: {} additionalProperties: false SoftwareRequirement: anyOf: - $ref: '#/definitions/SoftwareRequirementMap' - type: object properties: {} additionalProperties: false InitialWorkDirRequirement: anyOf: - $ref: '#/definitions/InitialWorkDirRequirementMap' - type: object properties: {} additionalProperties: false EnvVarRequirement: anyOf: - $ref: '#/definitions/EnvVarRequirementMap' - type: object properties: {} additionalProperties: false ShellCommandRequirement: anyOf: - $ref: '#/definitions/ShellCommandRequirementMap' - type: object properties: {} additionalProperties: false ResourceRequirement: anyOf: - $ref: '#/definitions/ResourceRequirementMap' - type: object properties: {} additionalProperties: false WorkReuse: anyOf: - $ref: '#/definitions/WorkReuseMap' - type: object properties: {} additionalProperties: false NetworkAccess: anyOf: - $ref: '#/definitions/NetworkAccessMap' - type: object properties: {} additionalProperties: false InplaceUpdateRequirement: anyOf: - $ref: '#/definitions/InplaceUpdateRequirementMap' - type: object properties: {} additionalProperties: false ToolTimeLimit: anyOf: - $ref: '#/definitions/ToolTimeLimitMap' - type: object properties: {} additionalProperties: false SubworkflowFeatureRequirement: anyOf: - $ref: '#/definitions/SubworkflowFeatureRequirementMap' - type: object properties: {} additionalProperties: false ScatterFeatureRequirement: anyOf: - $ref: '#/definitions/ScatterFeatureRequirementMap' - type: object properties: {} additionalProperties: false MultipleInputFeatureRequirement: anyOf: - $ref: '#/definitions/MultipleInputFeatureRequirementMap' - type: object properties: {} additionalProperties: false StepInputExpressionRequirement: anyOf: - $ref: '#/definitions/StepInputExpressionRequirementMap' - type: object properties: {} additionalProperties: false additionalProperties: false id: description: |- The unique identifier for this object. Only useful for `$graph` at `Process` level. Should not be exposed to users in graphical or terminal user interfaces. type: string inputs: description: |- Defines the input parameters of the process. 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 to build a user interface for constructing the input object. When accepting an input object, all input parameters must have a value. If an input parameter is missing from the input object, it must be assigned a value of `null` (or the value of `default` for that parameter, if provided) for the purposes of validation and evaluation of expressions. oneOf: - items: $ref: '#/definitions/OperationInputParameter' type: array - patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: oneOf: - $ref: '#/definitions/OperationInputParameter' - anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - items: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - type: string type: array - type: string description: Specify valid types of data that may be assigned to this parameter. - type: array items: oneOf: - type: string - $ref: '#/definitions/OperationInputParameter' type: object intent: description: |- An identifier for the type of computational operation, of this Process. Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for [`CommandLineTool`](CommandLineTool.html#CommandLineTool), [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool). If provided, then this must be an IRI of a concept node that represents the type of operation, preferably defined within an ontology. For example, in the domain of bioinformatics, one can use an IRI from the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), like [Alignment](http://edamontology.org/operation_2928), or [Clustering](http://edamontology.org/operation_3432); or a more specific Operation concept like [Split read mapping](http://edamontology.org/operation_3199). items: type: string type: array label: description: A short, human-readable label of this object. type: string outputs: description: |- Defines the parameters representing the output of the process. May be used to generate and/or validate the output object. oneOf: - items: $ref: '#/definitions/OperationOutputParameter' type: array - patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: oneOf: - $ref: '#/definitions/OperationOutputParameter' - anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - items: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - type: string type: array - type: string description: Specify valid types of data that may be assigned to this parameter. - type: array items: oneOf: - type: string - $ref: '#/definitions/OperationOutputParameter' type: object requirements: description: |- Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. 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. oneOf: - items: anyOf: - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' - $ref: '#/definitions/InlineJavascriptRequirement' - $ref: '#/definitions/SchemaDefRequirement' - $ref: '#/definitions/LoadListingRequirement' - $ref: '#/definitions/DockerRequirement' - $ref: '#/definitions/SoftwareRequirement' - $ref: '#/definitions/InitialWorkDirRequirement' - $ref: '#/definitions/EnvVarRequirement' - $ref: '#/definitions/ShellCommandRequirement' - $ref: '#/definitions/ResourceRequirement' - $ref: '#/definitions/WorkReuse' - $ref: '#/definitions/NetworkAccess' - $ref: '#/definitions/InplaceUpdateRequirement' - $ref: '#/definitions/ToolTimeLimit' - $ref: '#/definitions/SubworkflowFeatureRequirement' - $ref: '#/definitions/ScatterFeatureRequirement' - $ref: '#/definitions/MultipleInputFeatureRequirement' - $ref: '#/definitions/StepInputExpressionRequirement' type: array - type: object properties: InlineJavascriptRequirement: anyOf: - $ref: '#/definitions/InlineJavascriptRequirementMap' - type: object properties: {} additionalProperties: false SchemaDefRequirement: anyOf: - $ref: '#/definitions/SchemaDefRequirementMap' - type: object properties: {} additionalProperties: false LoadListingRequirement: anyOf: - $ref: '#/definitions/LoadListingRequirementMap' - type: object properties: {} additionalProperties: false DockerRequirement: anyOf: - $ref: '#/definitions/DockerRequirementMap' - type: object properties: {} additionalProperties: false SoftwareRequirement: anyOf: - $ref: '#/definitions/SoftwareRequirementMap' - type: object properties: {} additionalProperties: false InitialWorkDirRequirement: anyOf: - $ref: '#/definitions/InitialWorkDirRequirementMap' - type: object properties: {} additionalProperties: false EnvVarRequirement: anyOf: - $ref: '#/definitions/EnvVarRequirementMap' - type: object properties: {} additionalProperties: false ShellCommandRequirement: anyOf: - $ref: '#/definitions/ShellCommandRequirementMap' - type: object properties: {} additionalProperties: false ResourceRequirement: anyOf: - $ref: '#/definitions/ResourceRequirementMap' - type: object properties: {} additionalProperties: false WorkReuse: anyOf: - $ref: '#/definitions/WorkReuseMap' - type: object properties: {} additionalProperties: false NetworkAccess: anyOf: - $ref: '#/definitions/NetworkAccessMap' - type: object properties: {} additionalProperties: false InplaceUpdateRequirement: anyOf: - $ref: '#/definitions/InplaceUpdateRequirementMap' - type: object properties: {} additionalProperties: false ToolTimeLimit: anyOf: - $ref: '#/definitions/ToolTimeLimitMap' - type: object properties: {} additionalProperties: false SubworkflowFeatureRequirement: anyOf: - $ref: '#/definitions/SubworkflowFeatureRequirementMap' - type: object properties: {} additionalProperties: false ScatterFeatureRequirement: anyOf: - $ref: '#/definitions/ScatterFeatureRequirementMap' - type: object properties: {} additionalProperties: false MultipleInputFeatureRequirement: anyOf: - $ref: '#/definitions/MultipleInputFeatureRequirementMap' - type: object properties: {} additionalProperties: false StepInputExpressionRequirement: anyOf: - $ref: '#/definitions/StepInputExpressionRequirementMap' - type: object properties: {} additionalProperties: false additionalProperties: false required: - class - inputs - outputs type: object OperationInputParameter: additionalProperties: false description: Describe an input parameter of an operation. properties: default: description: |- The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before evaluating expressions (e.g. dependent `valueFrom` fields). doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. format: anyOf: - items: type: string type: array - type: string description: |- Only valid when `type: File` or is an array of `items: File`. This must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferably defined within an ontology. If no ontology is available, file formats may be tested by exact match. id: description: The unique identifier for this object. type: string label: description: A short, human-readable label of this object. type: string loadContents: description: |- Only valid when `type: File` or is an array of `items: File`. If true, the file (or each file in the array) must be a UTF-8 text file 64 KiB or smaller, and the implementation must read the entire contents of the file (or file array) and place it in the `contents` field of the File object for use by expressions. If the size of the file is greater than 64 KiB, the implementation must raise a fatal error. type: boolean loadListing: description: |- Only valid when `type: Directory` or is an array of `items: Directory`. Specify the desired behavior for loading the `listing` field of a Directory object for use by expressions. The order of precedence for loadListing is: 1. `loadListing` on an individual parameter 2. Inherited from `LoadListingRequirement` 3. By default: `no_listing` enum: - deep_listing - no_listing - shallow_listing type: string secondaryFiles: anyOf: - $ref: '#/definitions/SecondaryFileSchema' - items: $ref: '#/definitions/SecondaryFileSchema' type: array description: |- Only valid when `type: File` or is an array of `items: File`. Provides a pattern or expression specifying files or directories that should be included alongside the primary file. Secondary files may be required or optional. When not explicitly specified, secondary files specified for `inputs` are required and `outputs` are optional. An implementation must include matching Files and Directories in the `secondaryFiles` property of the primary file. These Files and Directories must be transferred and staged alongside the primary file. An implementation may fail workflow execution if a required secondary file does not exist. If the value is an expression, the value of `self` in the expression must be the primary input or output File object to which this binding applies. The `basename`, `nameroot` and `nameext` fields must be present in `self`. For `CommandLineTool` outputs the `path` field must also be present. The expression must return a filename string relative to the path to the primary File, a File or Directory object with either `path` or `location` and `basename` fields set, or an array consisting of strings or File or Directory objects. It is legal to reference an unchanged File or Directory object taken from input as a secondaryFile. The expression may return "null" in which case there is no secondaryFile from that expression. To work on non-filename-preserving storage systems, portable tool descriptions should avoid constructing new values from `location`, but should construct relative references using `basename` or `nameroot` instead. If a value in `secondaryFiles` is a string that is not an expression, it specifies that the following pattern should be applied to the path of the primary file to yield a filename relative to the primary File: 1. If string ends with `?` character, remove the last `?` and mark the resulting secondary file as optional. 2. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 3. Append the remainder of the string to the end of the file path. streamable: description: |- Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. type: boolean type: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - items: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - type: string type: array - type: string description: Specify valid types of data that may be assigned to this parameter. required: - type type: object OperationOutputParameter: additionalProperties: false description: Describe an output parameter of an operation. properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. format: description: |- Only valid when `type: File` or is an array of `items: File`. This is the file format that will be assigned to the output File object. type: string id: description: The unique identifier for this object. type: string label: description: A short, human-readable label of this object. type: string secondaryFiles: anyOf: - $ref: '#/definitions/SecondaryFileSchema' - items: $ref: '#/definitions/SecondaryFileSchema' type: array description: |- Only valid when `type: File` or is an array of `items: File`. Provides a pattern or expression specifying files or directories that should be included alongside the primary file. Secondary files may be required or optional. When not explicitly specified, secondary files specified for `inputs` are required and `outputs` are optional. An implementation must include matching Files and Directories in the `secondaryFiles` property of the primary file. These Files and Directories must be transferred and staged alongside the primary file. An implementation may fail workflow execution if a required secondary file does not exist. If the value is an expression, the value of `self` in the expression must be the primary input or output File object to which this binding applies. The `basename`, `nameroot` and `nameext` fields must be present in `self`. For `CommandLineTool` outputs the `path` field must also be present. The expression must return a filename string relative to the path to the primary File, a File or Directory object with either `path` or `location` and `basename` fields set, or an array consisting of strings or File or Directory objects. It is legal to reference an unchanged File or Directory object taken from input as a secondaryFile. The expression may return "null" in which case there is no secondaryFile from that expression. To work on non-filename-preserving storage systems, portable tool descriptions should avoid constructing new values from `location`, but should construct relative references using `basename` or `nameroot` instead. If a value in `secondaryFiles` is a string that is not an expression, it specifies that the following pattern should be applied to the path of the primary file to yield a filename relative to the primary File: 1. If string ends with `?` character, remove the last `?` and mark the resulting secondary file as optional. 2. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 3. Append the remainder of the string to the end of the file path. streamable: description: |- Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. type: boolean type: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - items: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - type: string type: array - type: string description: Specify valid types of data that may be assigned to this parameter. required: - type type: object OutputArraySchema: additionalProperties: false description: Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputArraySchema properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. items: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - items: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - type: string type: array - type: string description: Defines the type of the array elements. label: description: A short, human-readable label of this object. type: string name: description: The identifier for this type type: string type: const: array description: Must be `array` type: string required: - items - type type: object OutputEnumSchema: additionalProperties: false description: Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputEnumSchema properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. label: description: A short, human-readable label of this object. type: string name: description: The identifier for this type type: string symbols: description: Defines the set of valid symbols. items: type: string type: array type: const: enum description: Must be `enum` type: string required: - symbols - type type: object OutputRecordField: description: Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordField oneOf: - additionalProperties: false properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. format: description: |- Only valid when `type: File` or is an array of `items: File`. This is the file format that will be assigned to the output File object. type: string label: description: A short, human-readable label of this object. type: string name: description: The name of the field type: string secondaryFiles: anyOf: - $ref: '#/definitions/SecondaryFileSchema' - items: $ref: '#/definitions/SecondaryFileSchema' type: array description: |- Only valid when `type: File` or is an array of `items: File`. Provides a pattern or expression specifying files or directories that should be included alongside the primary file. Secondary files may be required or optional. When not explicitly specified, secondary files specified for `inputs` are required and `outputs` are optional. An implementation must include matching Files and Directories in the `secondaryFiles` property of the primary file. These Files and Directories must be transferred and staged alongside the primary file. An implementation may fail workflow execution if a required secondary file does not exist. If the value is an expression, the value of `self` in the expression must be the primary input or output File object to which this binding applies. The `basename`, `nameroot` and `nameext` fields must be present in `self`. For `CommandLineTool` outputs the `path` field must also be present. The expression must return a filename string relative to the path to the primary File, a File or Directory object with either `path` or `location` and `basename` fields set, or an array consisting of strings or File or Directory objects. It is legal to reference an unchanged File or Directory object taken from input as a secondaryFile. The expression may return "null" in which case there is no secondaryFile from that expression. To work on non-filename-preserving storage systems, portable tool descriptions should avoid constructing new values from `location`, but should construct relative references using `basename` or `nameroot` instead. If a value in `secondaryFiles` is a string that is not an expression, it specifies that the following pattern should be applied to the path of the primary file to yield a filename relative to the primary File: 1. If string ends with `?` character, remove the last `?` and mark the resulting secondary file as optional. 2. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 3. Append the remainder of the string to the end of the file path. streamable: description: |- Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. type: boolean type: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - items: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - type: string type: array - type: string description: The field type required: - name - type type: object - type: array items: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - items: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - type: string type: array - type: string description: The field type OutputRecordSchema: additionalProperties: false description: Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordSchema properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. fields: description: Defines the fields of the record. oneOf: - items: $ref: '#/definitions/OutputRecordField' type: array - patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: $ref: '#/definitions/OutputRecordFieldMap' type: object label: description: A short, human-readable label of this object. type: string name: description: The identifier for this type type: string type: const: record description: Must be `record` type: string required: - type type: object ResourceRequirement: additionalProperties: false description: |- Specify basic hardware resource requirements. "min" is the minimum amount of a resource that must be reserved to schedule a job. If "min" cannot be satisfied, the job should not be run. "max" is the maximum amount of a resource that the job shall be allocated. If a node has sufficient resources, multiple jobs may be scheduled on a single node provided each job's "max" resource requirements are met. If a job attempts to exceed its resource allocation, an implementation may deny additional resources, which may result in job failure. If both "min" and "max" are specified, an implementation may choose to allocate any amount between "min" and "max", with the actual allocation provided in the `runtime` object. If "min" is specified but "max" is not, then "max" == "min" If "max" is specified by "min" is not, then "min" == "max". It is an error if max < min. It is an error if the value of any of these fields is negative. If neither "min" nor "max" is specified for a resource, use the default values below. properties: class: const: ResourceRequirement description: Always 'ResourceRequirement' type: string coresMax: description: |- Maximum reserved number of CPU cores. See `coresMin` for discussion about fractional CPU requests. type: - string - number coresMin: description: |- Minimum reserved number of CPU cores (default is 1). May be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 ≈ 3). Processes can only share a core allocation if the sum of each of their `ramMax`, `tmpdirMax`, and `outdirMax` requests also do not exceed the capacity of the node. Processes sharing a core must have the same level of isolation (typically a container or VM) that they would normally have. The reported number of CPU cores reserved for the process, which is available to expressions on the CommandLineTool as `runtime.cores`, must be a non-zero integer, and may be calculated by rounding up the cores request to the next whole number. Scheduling systems may allocate fractional CPU resources by setting quotas or scheduling weights. Scheduling systems that do not support fractional CPUs may round up the request to the next whole number. type: - string - number outdirMax: description: |- Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) See `outdirMin` for discussion about fractional storage requests. type: - string - number outdirMin: description: |- Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) (default is 1024) May be a fractional value. If so, the actual storage request must be rounded up to the next whole number. The reported amount of storage reserved for the process, which is available to expressions on the CommandLineTool as `runtime.outdirSize`, must be a non-zero integer. type: - string - number ramMax: description: |- Maximum reserved RAM in mebibytes (2**20) See `ramMin` for discussion about fractional RAM requests. type: - string - number ramMin: description: |- Minimum reserved RAM in mebibytes (2**20) (default is 256) May be a fractional value. If so, the actual RAM request must be rounded up to the next whole number. The reported amount of RAM reserved for the process, which is available to expressions on the CommandLineTool as `runtime.ram`, must be a non-zero integer. type: - string - number tmpdirMax: description: |- Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) See `tmpdirMin` for discussion about fractional storage requests. type: - string - number tmpdirMin: description: |- Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) (default is 1024) May be a fractional value. If so, the actual storage request must be rounded up to the next whole number. The reported amount of storage reserved for the process, which is available to expressions on the CommandLineTool as `runtime.tmpdirSize`, must be a non-zero integer. type: - string - number required: - class type: object ScatterFeatureRequirement: additionalProperties: false description: |- Indicates that the workflow platform must support the `scatter` and `scatterMethod` fields of [WorkflowStep](#WorkflowStep). properties: class: const: ScatterFeatureRequirement description: Always 'ScatterFeatureRequirement' type: string required: - class type: object SchemaDefRequirement: additionalProperties: false description: |- This field consists of an array of type definitions which must be used when interpreting the `inputs` and `outputs` fields. When a `type` field contains a IRI, the implementation must check if the type is defined in `schemaDefs` and use that definition. If the type is not found in `schemaDefs`, it is an error. The entries in `schemaDefs` must be processed in the order listed such that later schema definitions may refer to earlier schema definitions. - **Type definitions are allowed for `enum` and `record` types only.** - Type definitions may be shared by defining them in a file and then `$include`-ing them in the `types` field. - A file can contain a list of type definitions properties: class: const: SchemaDefRequirement description: Always 'SchemaDefRequirement' type: string types: description: The list of type definitions. items: anyOf: - anyOf: - $ref: '#/definitions/CommandInputArraySchema' - $ref: '#/definitions/CommandInputRecordSchema' - $ref: '#/definitions/CommandInputEnumSchema' - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' type: array required: - class - types type: object SecondaryFileSchema: description: |- Secondary files are specified using the following micro-DSL for secondary files: * If the value is a string, it is transformed to an object with two fields `pattern` and `required` * By default, the value of `required` is `null` (this indicates default behavior, which may be based on the context) * If the value ends with a question mark `?` the question mark is stripped off and the value of the field `required` is set to `False` * The remaining value is assigned to the field `pattern` For implementation details and examples, please see [this section](SchemaSalad.html#Domain_Specific_Language_for_secondary_files) in the Schema Salad specification. oneOf: - additionalProperties: false properties: pattern: description: |- Provides a pattern or expression specifying files or directories that should be included alongside the primary file. If the value is an expression, the value of `self` in the expression must be the primary input or output File object to which this binding applies. The `basename`, `nameroot` and `nameext` fields must be present in `self`. For `CommandLineTool` inputs the `location` field must also be present. For `CommandLineTool` outputs the `path` field must also be present. If secondary files were included on an input File object as part of the Process invocation, they must also be present in `secondaryFiles` on `self`. The expression must return either: a filename string relative to the path to the primary File, a File or Directory object (`class: File` or `class: Directory`) with either `location` (for inputs) or `path` (for outputs) and `basename` fields set, or an array consisting of strings or File or Directory objects as previously described. It is legal to use `location` from a File or Directory object passed in as input, including `location` from secondary files on `self`. If an expression returns a File object with the same `location` but a different `basename` as a secondary file that was passed in, the expression result takes precedence. Setting the basename with an expression this way affects the `path` where the secondary file will be staged to in the CommandLineTool. The expression may return "null" in which case there is no secondary file from that expression. To work on non-filename-preserving storage systems, portable tool descriptions should treat `location` as an [opaque identifier](#opaque-strings) and avoid constructing new values from `location`, but should construct relative references using `basename` or `nameroot` instead, or propagate `location` from defined inputs. If a value in `secondaryFiles` is a string that is not an expression, it specifies that the following pattern should be applied to the path of the primary file to yield a filename relative to the primary File: 1. If string ends with `?` character, remove the last `?` and mark the resulting secondary file as optional. 2. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 3. Append the remainder of the string to the end of the file path. type: string required: description: |- An implementation must not fail workflow execution if `required` is set to `false` and the expected secondary file does not exist. Default value for `required` field is `true` for secondary files on input and `false` for secondary files on output. type: - string - boolean required: - pattern type: object - type: string ShellCommandRequirement: additionalProperties: false description: |- Modify the behavior of CommandLineTool to generate a single string containing a shell command line. Each item in the `arguments` list must be joined into a string separated by single spaces and quoted to prevent interpretation by the shell, unless `CommandLineBinding` for that argument contains `shellQuote: false`. If `shellQuote: false` is specified, the argument is joined into the command string without quoting, which allows the use of shell metacharacters such as `|` for pipes. properties: class: const: ShellCommandRequirement description: Always 'ShellCommandRequirement' type: string required: - class type: object SoftwarePackage: additionalProperties: false description: Auto-generated class implementation for https://w3id.org/cwl/cwl#SoftwarePackage properties: package: description: |- The name of the software to be made available. If the name is common, inconsistent, or otherwise ambiguous it should be combined with one or more identifiers in the `specs` field. type: string specs: description: |- One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s identifying resources for installing or enabling the software named in the `package` field. Implementations may provide resolvers which map these software identifier IRIs to some configuration action; or they can use only the name from the `package` field on a best effort basis. For example, the IRI https://packages.debian.org/bowtie could be resolved with `apt-get install bowtie`. The IRI https://anaconda.org/bioconda/bowtie could be resolved with `conda install -c bioconda bowtie`. IRIs can also be system independent and used to map to a specific software installation or selection mechanism. Using [RRID](https://www.identifiers.org/rrid/) as an example: https://identifiers.org/rrid/RRID:SCR_005476 could be fulfilled using the above-mentioned Debian or bioconda package, a local installation managed by [Environment Modules](https://modules.sourceforge.net/), or any other mechanism the platform chooses. IRIs can also be from identifier sources that are discipline specific yet still system independent. As an example, the equivalent [ELIXIR Tools and Data Service Registry](https://bio.tools) IRI to the previous RRID example is https://bio.tools/tool/bowtie2/version/2.2.8. If supported by a given registry, implementations are encouraged to query these system independent software identifier IRIs directly for links to packaging systems. A site specific IRI can be listed as well. For example, an academic computing cluster using Environment Modules could list the IRI `https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that `module load bowtie-tbb/1.1.2` should be executed to make available `bowtie` version 1.1.2 compiled with the TBB library prior to running the accompanying Workflow or CommandLineTool. Note that the example IRI is specific to a particular institution and computing environment as the Environment Modules system does not have a common namespace or standardized naming convention. This last example is the least portable and should only be used if mechanisms based off of the `package` field or more generic IRIs are unavailable or unsuitable. While harmless to other sites, site specific software IRIs should be left out of shared CWL descriptions to avoid clutter. items: type: string type: array version: description: |- The (optional) versions of the software that are known to be compatible. items: type: string type: array required: - package type: object SoftwareRequirement: additionalProperties: false description: |- A list of software packages that should be configured in the environment of the defined process. properties: class: const: SoftwareRequirement description: Always 'SoftwareRequirement' type: string packages: description: The list of software to be configured. items: anyOf: - $ref: '#/definitions/SoftwarePackage' - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' type: array required: - class - packages type: object StepInputExpressionRequirement: additionalProperties: false description: |- Indicate that the workflow platform must support the `valueFrom` field of [WorkflowStepInput](#WorkflowStepInput). properties: class: const: StepInputExpressionRequirement description: Always 'StepInputExpressionRequirement' type: string required: - class type: object SubworkflowFeatureRequirement: additionalProperties: false description: |- Indicates that the workflow platform must support nested workflows in the `run` field of [WorkflowStep](#WorkflowStep). properties: class: const: SubworkflowFeatureRequirement description: Always 'SubworkflowFeatureRequirement' type: string required: - class type: object T: additionalProperties: false type: object ToolTimeLimit: additionalProperties: false description: |- Set an upper limit on the execution time of a CommandLineTool. A CommandLineTool whose execution duration exceeds the time limit may be preemptively terminated and considered failed. May also be used by batch systems to make scheduling decisions. The execution duration excludes external operations, such as staging of files, pulling a docker image etc, and only counts wall-time for the execution of the command line itself. properties: class: const: ToolTimeLimit description: Always 'ToolTimeLimit' type: string timelimit: description: |- The time limit, in seconds. A time limit of zero means no time limit. Negative time limits are an error. type: - string - number required: - class - timelimit type: object WorkReuse: additionalProperties: false description: |- For implementations that support reusing output from past work (on the assumption that same code and same input produce same results), control whether to enable or disable the reuse behavior for a particular tool or step (to accommodate situations where that assumption is incorrect). A reused step is not executed but instead returns the same output as the original execution. If `WorkReuse` is not specified, correct tools should assume it is enabled by default. properties: class: const: WorkReuse description: Always 'WorkReuse' type: string enableReuse: type: - string - boolean required: - class - enableReuse type: object Workflow: description: |- 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 `outputSource` field on [workflow output parameters](#WorkflowOutputParameter). The `source` field on each workflow step input parameter expresses the data links that contribute to the value of the step input parameter (the "sink"). A workflow step can only begin execution when every data link connected to a step has been fulfilled. The `outputSource` field on each workflow step input parameter expresses the data links that contribute to the value of the workflow output parameter (the "sink"). Workflow execution cannot complete successfully until every data link connected to an output parameter has been fulfilled. ## 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. properties: class: const: Workflow type: string cwlVersion: description: |- CWL document version. Always required at the document root. Not required for a Process embedded inside another Process. enum: - draft-2 - draft-3 - draft-3.dev1 - draft-3.dev2 - draft-3.dev3 - draft-3.dev4 - draft-3.dev5 - draft-4.dev1 - draft-4.dev2 - draft-4.dev3 - v1.0 - v1.0.dev4 - v1.1 - v1.1.0-dev1 - v1.2 - v1.2.0-dev1 - v1.2.0-dev2 - v1.2.0-dev3 - v1.2.0-dev4 - v1.2.0-dev5 type: string doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. hints: description: |- Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. 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. oneOf: - items: anyOf: - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' - $ref: '#/definitions/InlineJavascriptRequirement' - $ref: '#/definitions/SchemaDefRequirement' - $ref: '#/definitions/LoadListingRequirement' - $ref: '#/definitions/DockerRequirement' - $ref: '#/definitions/SoftwareRequirement' - $ref: '#/definitions/InitialWorkDirRequirement' - $ref: '#/definitions/EnvVarRequirement' - $ref: '#/definitions/ShellCommandRequirement' - $ref: '#/definitions/ResourceRequirement' - $ref: '#/definitions/WorkReuse' - $ref: '#/definitions/NetworkAccess' - $ref: '#/definitions/InplaceUpdateRequirement' - $ref: '#/definitions/ToolTimeLimit' - $ref: '#/definitions/SubworkflowFeatureRequirement' - $ref: '#/definitions/ScatterFeatureRequirement' - $ref: '#/definitions/MultipleInputFeatureRequirement' - $ref: '#/definitions/StepInputExpressionRequirement' type: array - type: object properties: InlineJavascriptRequirement: anyOf: - $ref: '#/definitions/InlineJavascriptRequirementMap' - type: object properties: {} additionalProperties: false SchemaDefRequirement: anyOf: - $ref: '#/definitions/SchemaDefRequirementMap' - type: object properties: {} additionalProperties: false LoadListingRequirement: anyOf: - $ref: '#/definitions/LoadListingRequirementMap' - type: object properties: {} additionalProperties: false DockerRequirement: anyOf: - $ref: '#/definitions/DockerRequirementMap' - type: object properties: {} additionalProperties: false SoftwareRequirement: anyOf: - $ref: '#/definitions/SoftwareRequirementMap' - type: object properties: {} additionalProperties: false InitialWorkDirRequirement: anyOf: - $ref: '#/definitions/InitialWorkDirRequirementMap' - type: object properties: {} additionalProperties: false EnvVarRequirement: anyOf: - $ref: '#/definitions/EnvVarRequirementMap' - type: object properties: {} additionalProperties: false ShellCommandRequirement: anyOf: - $ref: '#/definitions/ShellCommandRequirementMap' - type: object properties: {} additionalProperties: false ResourceRequirement: anyOf: - $ref: '#/definitions/ResourceRequirementMap' - type: object properties: {} additionalProperties: false WorkReuse: anyOf: - $ref: '#/definitions/WorkReuseMap' - type: object properties: {} additionalProperties: false NetworkAccess: anyOf: - $ref: '#/definitions/NetworkAccessMap' - type: object properties: {} additionalProperties: false InplaceUpdateRequirement: anyOf: - $ref: '#/definitions/InplaceUpdateRequirementMap' - type: object properties: {} additionalProperties: false ToolTimeLimit: anyOf: - $ref: '#/definitions/ToolTimeLimitMap' - type: object properties: {} additionalProperties: false SubworkflowFeatureRequirement: anyOf: - $ref: '#/definitions/SubworkflowFeatureRequirementMap' - type: object properties: {} additionalProperties: false ScatterFeatureRequirement: anyOf: - $ref: '#/definitions/ScatterFeatureRequirementMap' - type: object properties: {} additionalProperties: false MultipleInputFeatureRequirement: anyOf: - $ref: '#/definitions/MultipleInputFeatureRequirementMap' - type: object properties: {} additionalProperties: false StepInputExpressionRequirement: anyOf: - $ref: '#/definitions/StepInputExpressionRequirementMap' - type: object properties: {} additionalProperties: false additionalProperties: false id: description: |- The unique identifier for this object. Only useful for `$graph` at `Process` level. Should not be exposed to users in graphical or terminal user interfaces. type: string inputs: description: |- Defines the input parameters of the process. 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 to build a user interface for constructing the input object. When accepting an input object, all input parameters must have a value. If an input parameter is missing from the input object, it must be assigned a value of `null` (or the value of `default` for that parameter, if provided) for the purposes of validation and evaluation of expressions. oneOf: - items: $ref: '#/definitions/WorkflowInputParameter' type: array - patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: oneOf: - $ref: '#/definitions/WorkflowInputParameter' - anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - items: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - type: string type: array - type: string description: Specify valid types of data that may be assigned to this parameter. - type: array items: oneOf: - type: string - $ref: '#/definitions/WorkflowInputParameter' type: object intent: description: |- An identifier for the type of computational operation, of this Process. Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for [`CommandLineTool`](CommandLineTool.html#CommandLineTool), [`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool). If provided, then this must be an IRI of a concept node that represents the type of operation, preferably defined within an ontology. For example, in the domain of bioinformatics, one can use an IRI from the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), like [Alignment](http://edamontology.org/operation_2928), or [Clustering](http://edamontology.org/operation_3432); or a more specific Operation concept like [Split read mapping](http://edamontology.org/operation_3199). items: type: string type: array label: description: A short, human-readable label of this object. type: string outputs: description: |- Defines the parameters representing the output of the process. May be used to generate and/or validate the output object. oneOf: - items: $ref: '#/definitions/WorkflowOutputParameter' type: array - patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: oneOf: - $ref: '#/definitions/WorkflowOutputParameter' - anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - items: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - type: string type: array - type: string description: Specify valid types of data that may be assigned to this parameter. - type: array items: oneOf: - type: string - $ref: '#/definitions/WorkflowOutputParameter' type: object requirements: description: |- Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this process. 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. oneOf: - items: anyOf: - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' - $ref: '#/definitions/InlineJavascriptRequirement' - $ref: '#/definitions/SchemaDefRequirement' - $ref: '#/definitions/LoadListingRequirement' - $ref: '#/definitions/DockerRequirement' - $ref: '#/definitions/SoftwareRequirement' - $ref: '#/definitions/InitialWorkDirRequirement' - $ref: '#/definitions/EnvVarRequirement' - $ref: '#/definitions/ShellCommandRequirement' - $ref: '#/definitions/ResourceRequirement' - $ref: '#/definitions/WorkReuse' - $ref: '#/definitions/NetworkAccess' - $ref: '#/definitions/InplaceUpdateRequirement' - $ref: '#/definitions/ToolTimeLimit' - $ref: '#/definitions/SubworkflowFeatureRequirement' - $ref: '#/definitions/ScatterFeatureRequirement' - $ref: '#/definitions/MultipleInputFeatureRequirement' - $ref: '#/definitions/StepInputExpressionRequirement' type: array - type: object properties: InlineJavascriptRequirement: anyOf: - $ref: '#/definitions/InlineJavascriptRequirementMap' - type: object properties: {} additionalProperties: false SchemaDefRequirement: anyOf: - $ref: '#/definitions/SchemaDefRequirementMap' - type: object properties: {} additionalProperties: false LoadListingRequirement: anyOf: - $ref: '#/definitions/LoadListingRequirementMap' - type: object properties: {} additionalProperties: false DockerRequirement: anyOf: - $ref: '#/definitions/DockerRequirementMap' - type: object properties: {} additionalProperties: false SoftwareRequirement: anyOf: - $ref: '#/definitions/SoftwareRequirementMap' - type: object properties: {} additionalProperties: false InitialWorkDirRequirement: anyOf: - $ref: '#/definitions/InitialWorkDirRequirementMap' - type: object properties: {} additionalProperties: false EnvVarRequirement: anyOf: - $ref: '#/definitions/EnvVarRequirementMap' - type: object properties: {} additionalProperties: false ShellCommandRequirement: anyOf: - $ref: '#/definitions/ShellCommandRequirementMap' - type: object properties: {} additionalProperties: false ResourceRequirement: anyOf: - $ref: '#/definitions/ResourceRequirementMap' - type: object properties: {} additionalProperties: false WorkReuse: anyOf: - $ref: '#/definitions/WorkReuseMap' - type: object properties: {} additionalProperties: false NetworkAccess: anyOf: - $ref: '#/definitions/NetworkAccessMap' - type: object properties: {} additionalProperties: false InplaceUpdateRequirement: anyOf: - $ref: '#/definitions/InplaceUpdateRequirementMap' - type: object properties: {} additionalProperties: false ToolTimeLimit: anyOf: - $ref: '#/definitions/ToolTimeLimitMap' - type: object properties: {} additionalProperties: false SubworkflowFeatureRequirement: anyOf: - $ref: '#/definitions/SubworkflowFeatureRequirementMap' - type: object properties: {} additionalProperties: false ScatterFeatureRequirement: anyOf: - $ref: '#/definitions/ScatterFeatureRequirementMap' - type: object properties: {} additionalProperties: false MultipleInputFeatureRequirement: anyOf: - $ref: '#/definitions/MultipleInputFeatureRequirementMap' - type: object properties: {} additionalProperties: false StepInputExpressionRequirement: anyOf: - $ref: '#/definitions/StepInputExpressionRequirementMap' - type: object properties: {} additionalProperties: false additionalProperties: false steps: description: |- The individual steps that make up the workflow. Each step is executed when all of its input data links are fulfilled. 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. oneOf: - items: $ref: '#/definitions/WorkflowStep' type: array - patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: $ref: '#/definitions/WorkflowStep' type: object required: - class - inputs - outputs - steps type: object WorkflowInputParameter: additionalProperties: false description: Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowInputParameter properties: default: description: |- The default value to use for this parameter if the parameter is missing from the input object, or if the value of the parameter in the input object is `null`. Default values are applied before evaluating expressions (e.g. dependent `valueFrom` fields). doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. format: anyOf: - items: type: string type: array - type: string description: |- Only valid when `type: File` or is an array of `items: File`. This must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferably defined within an ontology. If no ontology is available, file formats may be tested by exact match. id: description: The unique identifier for this object. type: string inputBinding: $ref: '#/definitions/InputBinding' description: |- Deprecated. Preserved for v1.0 backwards compatibility. Will be removed in CWL v2.0. Use `WorkflowInputParameter.loadContents` instead. label: description: A short, human-readable label of this object. type: string loadContents: description: |- Only valid when `type: File` or is an array of `items: File`. If true, the file (or each file in the array) must be a UTF-8 text file 64 KiB or smaller, and the implementation must read the entire contents of the file (or file array) and place it in the `contents` field of the File object for use by expressions. If the size of the file is greater than 64 KiB, the implementation must raise a fatal error. type: boolean loadListing: description: |- Only valid when `type: Directory` or is an array of `items: Directory`. Specify the desired behavior for loading the `listing` field of a Directory object for use by expressions. The order of precedence for loadListing is: 1. `loadListing` on an individual parameter 2. Inherited from `LoadListingRequirement` 3. By default: `no_listing` enum: - deep_listing - no_listing - shallow_listing type: string secondaryFiles: anyOf: - $ref: '#/definitions/SecondaryFileSchema' - items: $ref: '#/definitions/SecondaryFileSchema' type: array description: |- Only valid when `type: File` or is an array of `items: File`. Provides a pattern or expression specifying files or directories that should be included alongside the primary file. Secondary files may be required or optional. When not explicitly specified, secondary files specified for `inputs` are required and `outputs` are optional. An implementation must include matching Files and Directories in the `secondaryFiles` property of the primary file. These Files and Directories must be transferred and staged alongside the primary file. An implementation may fail workflow execution if a required secondary file does not exist. If the value is an expression, the value of `self` in the expression must be the primary input or output File object to which this binding applies. The `basename`, `nameroot` and `nameext` fields must be present in `self`. For `CommandLineTool` outputs the `path` field must also be present. The expression must return a filename string relative to the path to the primary File, a File or Directory object with either `path` or `location` and `basename` fields set, or an array consisting of strings or File or Directory objects. It is legal to reference an unchanged File or Directory object taken from input as a secondaryFile. The expression may return "null" in which case there is no secondaryFile from that expression. To work on non-filename-preserving storage systems, portable tool descriptions should avoid constructing new values from `location`, but should construct relative references using `basename` or `nameroot` instead. If a value in `secondaryFiles` is a string that is not an expression, it specifies that the following pattern should be applied to the path of the primary file to yield a filename relative to the primary File: 1. If string ends with `?` character, remove the last `?` and mark the resulting secondary file as optional. 2. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 3. Append the remainder of the string to the end of the file path. streamable: description: |- Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. type: boolean type: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - items: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - type: string type: array - type: string description: Specify valid types of data that may be assigned to this parameter. required: - type type: object WorkflowOutputParameter: additionalProperties: false description: |- 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. See [WorkflowStepInput](#WorkflowStepInput) for discussion of `linkMerge` and `pickValue`. properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. format: description: |- Only valid when `type: File` or is an array of `items: File`. This is the file format that will be assigned to the output File object. type: string id: description: The unique identifier for this object. type: string label: description: A short, human-readable label of this object. type: string linkMerge: description: |- The method to use to merge multiple sources into a single array. If not specified, the default method is "merge_nested". enum: - merge_flattened - merge_nested type: string outputSource: anyOf: - items: type: string type: array - type: string description: |- Specifies one or more names of an output from a workflow step (in the form `step_name/output_name` with a `/` separator`), or a workflow input name, that supply their value(s) to the output parameter. the output parameter. It is valid to reference workflow level inputs here. pickValue: description: The method to use to choose non-null elements among multiple sources. enum: - all_non_null - first_non_null - the_only_non_null type: string secondaryFiles: anyOf: - $ref: '#/definitions/SecondaryFileSchema' - items: $ref: '#/definitions/SecondaryFileSchema' type: array description: |- Only valid when `type: File` or is an array of `items: File`. Provides a pattern or expression specifying files or directories that should be included alongside the primary file. Secondary files may be required or optional. When not explicitly specified, secondary files specified for `inputs` are required and `outputs` are optional. An implementation must include matching Files and Directories in the `secondaryFiles` property of the primary file. These Files and Directories must be transferred and staged alongside the primary file. An implementation may fail workflow execution if a required secondary file does not exist. If the value is an expression, the value of `self` in the expression must be the primary input or output File object to which this binding applies. The `basename`, `nameroot` and `nameext` fields must be present in `self`. For `CommandLineTool` outputs the `path` field must also be present. The expression must return a filename string relative to the path to the primary File, a File or Directory object with either `path` or `location` and `basename` fields set, or an array consisting of strings or File or Directory objects. It is legal to reference an unchanged File or Directory object taken from input as a secondaryFile. The expression may return "null" in which case there is no secondaryFile from that expression. To work on non-filename-preserving storage systems, portable tool descriptions should avoid constructing new values from `location`, but should construct relative references using `basename` or `nameroot` instead. If a value in `secondaryFiles` is a string that is not an expression, it specifies that the following pattern should be applied to the path of the primary file to yield a filename relative to the primary File: 1. If string ends with `?` character, remove the last `?` and mark the resulting secondary file as optional. 2. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 3. Append the remainder of the string to the end of the file path. streamable: description: |- Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. type: boolean type: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - items: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - type: string type: array - type: string description: Specify valid types of data that may be assigned to this parameter. required: - type type: object WorkflowStep: additionalProperties: false description: |- 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 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. # Conditional execution (Optional) Conditional execution makes execution of a step conditional on an expression. A step that is not executed is "skipped". A skipped step produces `null` for all output parameters. The condition is evaluated after `scatter`, using the input object of each individual scatter job. This means over a set of scatter jobs, some may be executed and some may be skipped. When the results are gathered, skipped steps must be `null` in the output arrays. The `when` field controls conditional execution. This is an expression that must be evaluated with `inputs` bound to the step input object (or individual scatter job), and returns a boolean value. It is an error if this expression returns a value other than `true` or `false`. Conditionals in CWL are an optional feature and are not required to be implemented by all consumers of CWL documents. An implementation that does not support conditionals must return a fatal error when attempting to execute a workflow that uses conditional constructs the implementation does not support. # 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). properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. hints: description: |- 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. items: {} type: array id: description: The unique identifier for this object. type: string in: description: |- 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. oneOf: - items: $ref: '#/definitions/WorkflowStepInput' type: array - patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: oneOf: - $ref: '#/definitions/WorkflowStepInput' - type: string - type: array items: oneOf: - type: string - $ref: '#/definitions/WorkflowStepInput' type: object label: description: A short, human-readable label of this object. type: string out: description: |- Defines the parameters representing the output of the process. May be used to generate and/or validate the output object. items: anyOf: - $ref: '#/definitions/WorkflowStepOutput' - type: string type: array requirements: description: |- 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. oneOf: - items: anyOf: - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' - $ref: '#/definitions/InlineJavascriptRequirement' - $ref: '#/definitions/SchemaDefRequirement' - $ref: '#/definitions/LoadListingRequirement' - $ref: '#/definitions/DockerRequirement' - $ref: '#/definitions/SoftwareRequirement' - $ref: '#/definitions/InitialWorkDirRequirement' - $ref: '#/definitions/EnvVarRequirement' - $ref: '#/definitions/ShellCommandRequirement' - $ref: '#/definitions/ResourceRequirement' - $ref: '#/definitions/WorkReuse' - $ref: '#/definitions/NetworkAccess' - $ref: '#/definitions/InplaceUpdateRequirement' - $ref: '#/definitions/ToolTimeLimit' - $ref: '#/definitions/SubworkflowFeatureRequirement' - $ref: '#/definitions/ScatterFeatureRequirement' - $ref: '#/definitions/MultipleInputFeatureRequirement' - $ref: '#/definitions/StepInputExpressionRequirement' type: array - type: object properties: InlineJavascriptRequirement: anyOf: - $ref: '#/definitions/InlineJavascriptRequirementMap' - type: object properties: {} additionalProperties: false SchemaDefRequirement: anyOf: - $ref: '#/definitions/SchemaDefRequirementMap' - type: object properties: {} additionalProperties: false LoadListingRequirement: anyOf: - $ref: '#/definitions/LoadListingRequirementMap' - type: object properties: {} additionalProperties: false DockerRequirement: anyOf: - $ref: '#/definitions/DockerRequirementMap' - type: object properties: {} additionalProperties: false SoftwareRequirement: anyOf: - $ref: '#/definitions/SoftwareRequirementMap' - type: object properties: {} additionalProperties: false InitialWorkDirRequirement: anyOf: - $ref: '#/definitions/InitialWorkDirRequirementMap' - type: object properties: {} additionalProperties: false EnvVarRequirement: anyOf: - $ref: '#/definitions/EnvVarRequirementMap' - type: object properties: {} additionalProperties: false ShellCommandRequirement: anyOf: - $ref: '#/definitions/ShellCommandRequirementMap' - type: object properties: {} additionalProperties: false ResourceRequirement: anyOf: - $ref: '#/definitions/ResourceRequirementMap' - type: object properties: {} additionalProperties: false WorkReuse: anyOf: - $ref: '#/definitions/WorkReuseMap' - type: object properties: {} additionalProperties: false NetworkAccess: anyOf: - $ref: '#/definitions/NetworkAccessMap' - type: object properties: {} additionalProperties: false InplaceUpdateRequirement: anyOf: - $ref: '#/definitions/InplaceUpdateRequirementMap' - type: object properties: {} additionalProperties: false ToolTimeLimit: anyOf: - $ref: '#/definitions/ToolTimeLimitMap' - type: object properties: {} additionalProperties: false SubworkflowFeatureRequirement: anyOf: - $ref: '#/definitions/SubworkflowFeatureRequirementMap' - type: object properties: {} additionalProperties: false ScatterFeatureRequirement: anyOf: - $ref: '#/definitions/ScatterFeatureRequirementMap' - type: object properties: {} additionalProperties: false MultipleInputFeatureRequirement: anyOf: - $ref: '#/definitions/MultipleInputFeatureRequirementMap' - type: object properties: {} additionalProperties: false StepInputExpressionRequirement: anyOf: - $ref: '#/definitions/StepInputExpressionRequirementMap' - type: object properties: {} additionalProperties: false additionalProperties: false run: anyOf: - $ref: '#/definitions/CommandLineTool' - $ref: '#/definitions/ExpressionTool' - $ref: '#/definitions/Workflow' - $ref: '#/definitions/Operation' - type: string description: |- Specifies the process to run. If `run` is a string, it must be an absolute IRI or a relative path from the primary document. scatter: anyOf: - items: type: string type: array - type: string scatterMethod: description: Required if `scatter` is an array of more than one element. enum: - dotproduct - flat_crossproduct - nested_crossproduct type: string when: description: |- 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. type: string required: - in - out - run type: object WorkflowStepInput: additionalProperties: false description: |- 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 additional 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 multiple inbound data links 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 both `linkMerge` and `pickValue` are null or not specified, and there is more than one element in the `source` array, the default method is "merge_nested". If both `linkMerge` and `pickValue` are null or not specified, and there is only a single element in the `source`, then the input parameter takes the scalar value from the single input link (it is *not* wrapped in a single-list). * **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. # Picking non-null values among inbound data links If present, `pickValue` specifies how to pick non-null values among inbound data links. `pickValue` is evaluated 1. Once all source values from upstream step or parameters are available. 2. After `linkMerge`. 3. Before `scatter` or `valueFrom`. This is specifically intended to be useful in combination with [conditional execution](#WorkflowStep), where several upstream steps may be connected to a single input (`source` is a list), and skipped steps produce null values. Static type checkers should check for type consistency after inferring what the type will be after `pickValue` is applied, just as they do currently for `linkMerge`. * **first_non_null** For the first level of a list input, pick the first non-null element. The result is a scalar. It is an error if there is no non-null element. Examples: * `[null, x, null, y] -> x` * `[null, [null], null, y] -> [null]` * `[null, null, null] -> Runtime Error` *Intended use case*: If-else pattern where the value comes either from a conditional step or from a default or fallback value. The conditional step(s) should be placed first in the list. * **the_only_non_null** For the first level of a list input, pick the single non-null element. The result is a scalar. It is an error if there is more than one non-null element. Examples: * `[null, x, null] -> x` * `[null, x, null, y] -> Runtime Error` * `[null, [null], null] -> [null]` * `[null, null, null] -> Runtime Error` *Intended use case*: Switch type patterns where developer considers more than one active code path as a workflow error (possibly indicating an error in writing `when` condition expressions). * **all_non_null** For the first level of a list input, pick all non-null values. The result is a list, which may be empty. Examples: * `[null, x, null] -> [x]` * `[x, null, y] -> [x, y]` * `[null, [x], [null]] -> [[x], [null]]` * `[null, null, null] -> []` *Intended use case*: It is valid to have more than one source, but sources are conditional, so null sources (from skipped steps) should be filtered out. properties: default: description: |- 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`. id: description: The unique identifier for this object. type: string label: description: A short, human-readable label of this object. type: string linkMerge: description: |- The method to use to merge multiple inbound links into a single array. If not specified, the default method is "merge_nested". enum: - merge_flattened - merge_nested type: string loadContents: description: |- Only valid when `type: File` or is an array of `items: File`. If true, the file (or each file in the array) must be a UTF-8 text file 64 KiB or smaller, and the implementation must read the entire contents of the file (or file array) and place it in the `contents` field of the File object for use by expressions. If the size of the file is greater than 64 KiB, the implementation must raise a fatal error. type: boolean loadListing: description: |- Only valid when `type: Directory` or is an array of `items: Directory`. Specify the desired behavior for loading the `listing` field of a Directory object for use by expressions. The order of precedence for loadListing is: 1. `loadListing` on an individual parameter 2. Inherited from `LoadListingRequirement` 3. By default: `no_listing` enum: - deep_listing - no_listing - shallow_listing type: string pickValue: description: The method to use to choose non-null elements among multiple sources. enum: - all_non_null - first_non_null - the_only_non_null type: string source: anyOf: - items: type: string type: array - type: string description: |- Specifies one or more workflow parameters that will provide input to the underlying step parameter. valueFrom: description: |- 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 assigned 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: string required: [] type: object WorkflowStepOutput: additionalProperties: false description: |- 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. properties: id: description: The unique identifier for this object. type: string required: [] type: object CWLImportManual: description: Represents an '$import' directive that should point toward another compatible CWL file to import where specified. The contents of the imported file should be relevant contextually where it is being imported $comment: The schema validation of the CWL will not itself perform the '$import' to resolve and validate its contents. Therefore, the complete schema will not be validated entirely, and could still be partially malformed. To ensure proper and exhaustive validation of a CWL definition with this schema, all '$import' directives should be resolved and extended beforehand type: object properties: $import: type: string required: - $import additionalProperties: false CWLIncludeManual: description: Represents an '$include' directive that should point toward another compatible CWL file to import where specified. The contents of the imported file should be relevant contextually where it is being imported $comment: The schema validation of the CWL will not itself perform the '$include' to resolve and validate its contents. Therefore, the complete schema will not be validated entirely, and could still be partially malformed. To ensure proper and exhaustive validation of a CWL definition with this schema, all '$include' directives should be resolved and extended beforehand type: object properties: $include: type: string required: - $include additionalProperties: false CWLDocumentMetadata: description: Metadata for a CWL document type: object properties: $namespaces: description: The namespaces used in the document type: object patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: type: string $schemas: description: The schemas used in the document type: array items: type: string patternProperties: ^\w+:.*$: type: object ^\w+:\/\/.*: type: object required: [] CommandInputRecordFieldMap: description: Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputRecordField oneOf: - additionalProperties: false properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. format: anyOf: - items: type: string type: array - type: string description: |- Only valid when `type: File` or is an array of `items: File`. This must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferably defined within an ontology. If no ontology is available, file formats may be tested by exact match. inputBinding: $ref: '#/definitions/CommandLineBinding' description: Describes how to turn this object into command line arguments. label: description: A short, human-readable label of this object. type: string loadContents: description: |- Only valid when `type: File` or is an array of `items: File`. If true, the file (or each file in the array) must be a UTF-8 text file 64 KiB or smaller, and the implementation must read the entire contents of the file (or file array) and place it in the `contents` field of the File object for use by expressions. If the size of the file is greater than 64 KiB, the implementation must raise a fatal error. type: boolean loadListing: description: |- Only valid when `type: Directory` or is an array of `items: Directory`. Specify the desired behavior for loading the `listing` field of a Directory object for use by expressions. The order of precedence for loadListing is: 1. `loadListing` on an individual parameter 2. Inherited from `LoadListingRequirement` 3. By default: `no_listing` enum: - deep_listing - no_listing - shallow_listing type: string name: description: The name of the field type: string secondaryFiles: anyOf: - $ref: '#/definitions/SecondaryFileSchema' - items: $ref: '#/definitions/SecondaryFileSchema' type: array description: |- Only valid when `type: File` or is an array of `items: File`. Provides a pattern or expression specifying files or directories that should be included alongside the primary file. Secondary files may be required or optional. When not explicitly specified, secondary files specified for `inputs` are required and `outputs` are optional. An implementation must include matching Files and Directories in the `secondaryFiles` property of the primary file. These Files and Directories must be transferred and staged alongside the primary file. An implementation may fail workflow execution if a required secondary file does not exist. If the value is an expression, the value of `self` in the expression must be the primary input or output File object to which this binding applies. The `basename`, `nameroot` and `nameext` fields must be present in `self`. For `CommandLineTool` outputs the `path` field must also be present. The expression must return a filename string relative to the path to the primary File, a File or Directory object with either `path` or `location` and `basename` fields set, or an array consisting of strings or File or Directory objects. It is legal to reference an unchanged File or Directory object taken from input as a secondaryFile. The expression may return "null" in which case there is no secondaryFile from that expression. To work on non-filename-preserving storage systems, portable tool descriptions should avoid constructing new values from `location`, but should construct relative references using `basename` or `nameroot` instead. If a value in `secondaryFiles` is a string that is not an expression, it specifies that the following pattern should be applied to the path of the primary file to yield a filename relative to the primary File: 1. If string ends with `?` character, remove the last `?` and mark the resulting secondary file as optional. 2. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 3. Append the remainder of the string to the end of the file path. streamable: description: |- Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. type: boolean type: anyOf: - $ref: '#/definitions/CommandInputArraySchema' - $ref: '#/definitions/CommandInputRecordSchema' - $ref: '#/definitions/CommandInputEnumSchema' - items: anyOf: - $ref: '#/definitions/CommandInputArraySchema' - $ref: '#/definitions/CommandInputRecordSchema' - $ref: '#/definitions/CommandInputEnumSchema' - type: string type: array - type: string description: The field type type: object required: - type - type: array items: anyOf: - $ref: '#/definitions/CommandInputArraySchema' - $ref: '#/definitions/CommandInputRecordSchema' - $ref: '#/definitions/CommandInputEnumSchema' - items: anyOf: - $ref: '#/definitions/CommandInputArraySchema' - $ref: '#/definitions/CommandInputRecordSchema' - $ref: '#/definitions/CommandInputEnumSchema' - type: string type: array - type: string description: The field type - type: string InputRecordFieldMap: description: Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordField oneOf: - additionalProperties: false properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. format: anyOf: - items: type: string type: array - type: string description: |- Only valid when `type: File` or is an array of `items: File`. This must be one or more IRIs of concept nodes that represents file formats which are allowed as input to this parameter, preferably defined within an ontology. If no ontology is available, file formats may be tested by exact match. label: description: A short, human-readable label of this object. type: string loadContents: description: |- Only valid when `type: File` or is an array of `items: File`. If true, the file (or each file in the array) must be a UTF-8 text file 64 KiB or smaller, and the implementation must read the entire contents of the file (or file array) and place it in the `contents` field of the File object for use by expressions. If the size of the file is greater than 64 KiB, the implementation must raise a fatal error. type: boolean loadListing: description: |- Only valid when `type: Directory` or is an array of `items: Directory`. Specify the desired behavior for loading the `listing` field of a Directory object for use by expressions. The order of precedence for loadListing is: 1. `loadListing` on an individual parameter 2. Inherited from `LoadListingRequirement` 3. By default: `no_listing` enum: - deep_listing - no_listing - shallow_listing type: string name: description: The name of the field type: string secondaryFiles: anyOf: - $ref: '#/definitions/SecondaryFileSchema' - items: $ref: '#/definitions/SecondaryFileSchema' type: array description: |- Only valid when `type: File` or is an array of `items: File`. Provides a pattern or expression specifying files or directories that should be included alongside the primary file. Secondary files may be required or optional. When not explicitly specified, secondary files specified for `inputs` are required and `outputs` are optional. An implementation must include matching Files and Directories in the `secondaryFiles` property of the primary file. These Files and Directories must be transferred and staged alongside the primary file. An implementation may fail workflow execution if a required secondary file does not exist. If the value is an expression, the value of `self` in the expression must be the primary input or output File object to which this binding applies. The `basename`, `nameroot` and `nameext` fields must be present in `self`. For `CommandLineTool` outputs the `path` field must also be present. The expression must return a filename string relative to the path to the primary File, a File or Directory object with either `path` or `location` and `basename` fields set, or an array consisting of strings or File or Directory objects. It is legal to reference an unchanged File or Directory object taken from input as a secondaryFile. The expression may return "null" in which case there is no secondaryFile from that expression. To work on non-filename-preserving storage systems, portable tool descriptions should avoid constructing new values from `location`, but should construct relative references using `basename` or `nameroot` instead. If a value in `secondaryFiles` is a string that is not an expression, it specifies that the following pattern should be applied to the path of the primary file to yield a filename relative to the primary File: 1. If string ends with `?` character, remove the last `?` and mark the resulting secondary file as optional. 2. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 3. Append the remainder of the string to the end of the file path. streamable: description: |- Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. type: boolean type: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - items: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - type: string type: array - type: string description: The field type type: object required: - type - type: array items: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - items: anyOf: - $ref: '#/definitions/InputRecordSchema' - $ref: '#/definitions/InputEnumSchema' - $ref: '#/definitions/InputArraySchema' - type: string type: array - type: string description: The field type - type: string CommandOutputRecordFieldMap: description: Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordField oneOf: - additionalProperties: false properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. format: description: |- Only valid when `type: File` or is an array of `items: File`. This is the file format that will be assigned to the output File object. type: string label: description: A short, human-readable label of this object. type: string name: description: The name of the field type: string outputBinding: $ref: '#/definitions/CommandOutputBinding' description: |- Describes how to generate this output object based on the files produced by a CommandLineTool secondaryFiles: anyOf: - $ref: '#/definitions/SecondaryFileSchema' - items: $ref: '#/definitions/SecondaryFileSchema' type: array description: |- Only valid when `type: File` or is an array of `items: File`. Provides a pattern or expression specifying files or directories that should be included alongside the primary file. Secondary files may be required or optional. When not explicitly specified, secondary files specified for `inputs` are required and `outputs` are optional. An implementation must include matching Files and Directories in the `secondaryFiles` property of the primary file. These Files and Directories must be transferred and staged alongside the primary file. An implementation may fail workflow execution if a required secondary file does not exist. If the value is an expression, the value of `self` in the expression must be the primary input or output File object to which this binding applies. The `basename`, `nameroot` and `nameext` fields must be present in `self`. For `CommandLineTool` outputs the `path` field must also be present. The expression must return a filename string relative to the path to the primary File, a File or Directory object with either `path` or `location` and `basename` fields set, or an array consisting of strings or File or Directory objects. It is legal to reference an unchanged File or Directory object taken from input as a secondaryFile. The expression may return "null" in which case there is no secondaryFile from that expression. To work on non-filename-preserving storage systems, portable tool descriptions should avoid constructing new values from `location`, but should construct relative references using `basename` or `nameroot` instead. If a value in `secondaryFiles` is a string that is not an expression, it specifies that the following pattern should be applied to the path of the primary file to yield a filename relative to the primary File: 1. If string ends with `?` character, remove the last `?` and mark the resulting secondary file as optional. 2. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 3. Append the remainder of the string to the end of the file path. streamable: description: |- Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. type: boolean type: anyOf: - $ref: '#/definitions/CommandOutputArraySchema' - $ref: '#/definitions/CommandOutputRecordSchema' - $ref: '#/definitions/CommandOutputEnumSchema' - items: anyOf: - $ref: '#/definitions/CommandOutputArraySchema' - $ref: '#/definitions/CommandOutputRecordSchema' - $ref: '#/definitions/CommandOutputEnumSchema' - type: string type: array - type: string description: The field type type: object required: - type - type: array items: anyOf: - $ref: '#/definitions/CommandOutputArraySchema' - $ref: '#/definitions/CommandOutputRecordSchema' - $ref: '#/definitions/CommandOutputEnumSchema' - items: anyOf: - $ref: '#/definitions/CommandOutputArraySchema' - $ref: '#/definitions/CommandOutputRecordSchema' - $ref: '#/definitions/CommandOutputEnumSchema' - type: string type: array - type: string description: The field type - type: string OutputRecordFieldMap: description: Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordField oneOf: - additionalProperties: false properties: doc: anyOf: - items: type: string type: array - type: string description: A documentation string for this object, or an array of strings which should be concatenated. format: description: |- Only valid when `type: File` or is an array of `items: File`. This is the file format that will be assigned to the output File object. type: string label: description: A short, human-readable label of this object. type: string name: description: The name of the field type: string secondaryFiles: anyOf: - $ref: '#/definitions/SecondaryFileSchema' - items: $ref: '#/definitions/SecondaryFileSchema' type: array description: |- Only valid when `type: File` or is an array of `items: File`. Provides a pattern or expression specifying files or directories that should be included alongside the primary file. Secondary files may be required or optional. When not explicitly specified, secondary files specified for `inputs` are required and `outputs` are optional. An implementation must include matching Files and Directories in the `secondaryFiles` property of the primary file. These Files and Directories must be transferred and staged alongside the primary file. An implementation may fail workflow execution if a required secondary file does not exist. If the value is an expression, the value of `self` in the expression must be the primary input or output File object to which this binding applies. The `basename`, `nameroot` and `nameext` fields must be present in `self`. For `CommandLineTool` outputs the `path` field must also be present. The expression must return a filename string relative to the path to the primary File, a File or Directory object with either `path` or `location` and `basename` fields set, or an array consisting of strings or File or Directory objects. It is legal to reference an unchanged File or Directory object taken from input as a secondaryFile. The expression may return "null" in which case there is no secondaryFile from that expression. To work on non-filename-preserving storage systems, portable tool descriptions should avoid constructing new values from `location`, but should construct relative references using `basename` or `nameroot` instead. If a value in `secondaryFiles` is a string that is not an expression, it specifies that the following pattern should be applied to the path of the primary file to yield a filename relative to the primary File: 1. If string ends with `?` character, remove the last `?` and mark the resulting secondary file as optional. 2. If string begins with one or more caret `^` characters, for each caret, remove the last file extension from the path (the last period `.` and all following characters). If there are no file extensions, the path is unchanged. 3. Append the remainder of the string to the end of the file path. streamable: description: |- Only valid when `type: File` or is an array of `items: File`. A value of `true` indicates that the file is read or written sequentially without seeking. An implementation may use this flag to indicate whether it is valid to stream file contents using a named pipe. Default: `false`. type: boolean type: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - items: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - type: string type: array - type: string description: The field type type: object required: - type - type: array items: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - items: anyOf: - $ref: '#/definitions/OutputRecordSchema' - $ref: '#/definitions/OutputEnumSchema' - $ref: '#/definitions/OutputArraySchema' - type: string type: array - type: string description: The field type - type: string InlineJavascriptRequirementMap: type: object properties: expressionLib: description: |- Additional code fragments that will also be inserted before executing the expression code. Allows for function definitions that may be called from CWL expressions. items: anyOf: - type: string - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' type: array required: [] description: |- Indicates that the workflow platform must support inline Javascript expressions. If this requirement is not present, the workflow platform must not perform expression interpolation. SchemaDefRequirementMap: type: object properties: types: description: The list of type definitions. items: anyOf: - anyOf: - $ref: '#/definitions/CommandInputArraySchema' - $ref: '#/definitions/CommandInputRecordSchema' - $ref: '#/definitions/CommandInputEnumSchema' - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' type: array required: - types description: |- This field consists of an array of type definitions which must be used when interpreting the `inputs` and `outputs` fields. When a `type` field contains a IRI, the implementation must check if the type is defined in `schemaDefs` and use that definition. If the type is not found in `schemaDefs`, it is an error. The entries in `schemaDefs` must be processed in the order listed such that later schema definitions may refer to earlier schema definitions. - **Type definitions are allowed for `enum` and `record` types only.** - Type definitions may be shared by defining them in a file and then `$include`-ing them in the `types` field. - A file can contain a list of type definitions LoadListingRequirementMap: type: object properties: loadListing: enum: - deep_listing - no_listing - shallow_listing type: string required: [] description: |- Specify the desired behavior for loading the `listing` field of a Directory object for use by expressions. DockerRequirementMap: type: object properties: dockerFile: description: Supply the contents of a Dockerfile which will be built using `docker build`. type: string dockerImageId: description: |- The image id that will be used for `docker run`. May be a human-readable image name or the image identifier hash. May be skipped if `dockerPull` is specified, in which case the `dockerPull` image id must be used. type: string dockerImport: description: Provide HTTP URL to download and gunzip a Docker images using `docker import. type: string dockerLoad: description: Specify an HTTP URL from which to download a Docker image using `docker load`. type: string dockerOutputDirectory: description: |- Set the designated output directory to a specific location inside the Docker container. type: string dockerPull: description: |- Specify a Docker image to retrieve using `docker pull`. Can contain the immutable digest to ensure an exact container is used: `dockerPull: ubuntu@sha256:45b23dee08af5e43a7fea6c4cf9c25ccf269ee113168c19722f87876677c5cb2` type: string required: [] description: |- Indicates that a workflow component should be run in a [Docker](https://docker.com) or Docker-compatible (such as [Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment and specifies how to fetch or build the image. If a CommandLineTool lists `DockerRequirement` under `hints` (or `requirements`), it may (or must) be run in the specified Docker container. The platform must first acquire or install the correct Docker image as specified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`. The platform must execute the tool in the container using `docker run` with the appropriate Docker image and tool command line. The workflow platform may provide input files and the designated output directory through the use of volume bind mounts. The platform should rewrite file paths in the input object to correspond to the Docker bind mounted locations. That is, the platform should rewrite values in the parameter context such as `runtime.outdir`, `runtime.tmpdir` and others to be valid paths within the container. The platform must ensure that `runtime.outdir` and `runtime.tmpdir` are distinct directories. When running a tool contained in Docker, the workflow platform must not assume anything about the contents of the Docker container, such as the presence or absence of specific software, except to assume that the generated command line represents a valid command within the runtime environment of the container. A container image may specify an [ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint) and/or [CMD](https://docs.docker.com/engine/reference/builder/#cmd). Command line arguments will be appended after all elements of ENTRYPOINT, and will override all elements specified using CMD (in other words, CMD is only used when the CommandLineTool definition produces an empty command line). Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility concerns of the implicit hidden execution point (For further discussion, see [https://doi.org/10.12688/f1000research.15140.1](https://doi.org/10.12688/f1000research.15140.1)). Portable CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD. CommandLineTools which do rely on ENTRYPOINT or CMD must list `DockerRequirement` in the `requirements` section. ## Interaction with other requirements If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a DockerRequirement, the environment variables must be provided to Docker using `--env` or `--env-file` and interact with the container's preexisting environment as defined by Docker. SoftwareRequirementMap: type: object properties: packages: description: The list of software to be configured. items: anyOf: - $ref: '#/definitions/SoftwarePackage' - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' type: array required: - packages description: |- A list of software packages that should be configured in the environment of the defined process. InitialWorkDirRequirementMap: type: object properties: listing: anyOf: - items: anyOf: - anyOf: - $ref: '#/definitions/Directory' - $ref: '#/definitions/File' - items: anyOf: - anyOf: - $ref: '#/definitions/Directory' - $ref: '#/definitions/File' - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' type: array - $ref: '#/definitions/Dirent' - type: string - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' type: array - type: string description: |- The list of files or subdirectories that must be staged prior to executing the command line tool. Return type of each expression must validate as `["null", File, Directory, Dirent, {type: array, items: [File, Directory]}]`. Each `File` or `Directory` that is returned by an Expression must be added to the designated output directory prior to executing the tool. Each `Dirent` record that is listed or returned by an expression specifies a file to be created or staged in the designated output directory prior to executing the tool. Expressions may return null, in which case they have no effect. Files or Directories which are listed in the input parameters and appear in the `InitialWorkDirRequirement` listing must have their `path` set to their staged location. If the same File or Directory appears more than once in the `InitialWorkDirRequirement` listing, the implementation must choose exactly one value for `path`; how this value is chosen is undefined. required: [] description: |- Define a list of files and subdirectories that must be staged by the workflow platform prior to executing the command line tool. Normally files are staged within the designated output directory. However, when running inside containers, files may be staged at arbitrary locations, see discussion for [`Dirent.entryname`](#Dirent). Together with `DockerRequirement.dockerOutputDirectory` it is possible to control the locations of both input and output files when running in containers. EnvVarRequirementMap: type: object properties: envDef: description: The list of environment variables. oneOf: - items: anyOf: - $ref: '#/definitions/EnvironmentDef' - $ref: '#/definitions/CWLImportManual' - $ref: '#/definitions/CWLIncludeManual' type: array - patternProperties: ^[_a-zA-Z][a-zA-Z0-9_-]*$: type: string required: - envDef description: |- Define a list of environment variables which will be set in the execution environment of the tool. See `EnvironmentDef` for details. ShellCommandRequirementMap: type: object properties: {} required: [] description: |- Modify the behavior of CommandLineTool to generate a single string containing a shell command line. Each item in the `arguments` list must be joined into a string separated by single spaces and quoted to prevent interpretation by the shell, unless `CommandLineBinding` for that argument contains `shellQuote: false`. If `shellQuote: false` is specified, the argument is joined into the command string without quoting, which allows the use of shell metacharacters such as `|` for pipes. ResourceRequirementMap: type: object properties: coresMax: description: |- Maximum reserved number of CPU cores. See `coresMin` for discussion about fractional CPU requests. type: - string - number coresMin: description: |- Minimum reserved number of CPU cores (default is 1). May be a fractional value to indicate to a scheduling algorithm that one core can be allocated to multiple jobs. For example, a value of 0.25 indicates that up to 4 jobs may run in parallel on 1 core. A value of 1.25 means that up to 3 jobs can run on a 4 core system (4/1.25 ≈ 3). Processes can only share a core allocation if the sum of each of their `ramMax`, `tmpdirMax`, and `outdirMax` requests also do not exceed the capacity of the node. Processes sharing a core must have the same level of isolation (typically a container or VM) that they would normally have. The reported number of CPU cores reserved for the process, which is available to expressions on the CommandLineTool as `runtime.cores`, must be a non-zero integer, and may be calculated by rounding up the cores request to the next whole number. Scheduling systems may allocate fractional CPU resources by setting quotas or scheduling weights. Scheduling systems that do not support fractional CPUs may round up the request to the next whole number. type: - string - number outdirMax: description: |- Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) See `outdirMin` for discussion about fractional storage requests. type: - string - number outdirMin: description: |- Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) (default is 1024) May be a fractional value. If so, the actual storage request must be rounded up to the next whole number. The reported amount of storage reserved for the process, which is available to expressions on the CommandLineTool as `runtime.outdirSize`, must be a non-zero integer. type: - string - number ramMax: description: |- Maximum reserved RAM in mebibytes (2**20) See `ramMin` for discussion about fractional RAM requests. type: - string - number ramMin: description: |- Minimum reserved RAM in mebibytes (2**20) (default is 256) May be a fractional value. If so, the actual RAM request must be rounded up to the next whole number. The reported amount of RAM reserved for the process, which is available to expressions on the CommandLineTool as `runtime.ram`, must be a non-zero integer. type: - string - number tmpdirMax: description: |- Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) See `tmpdirMin` for discussion about fractional storage requests. type: - string - number tmpdirMin: description: |- Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) (default is 1024) May be a fractional value. If so, the actual storage request must be rounded up to the next whole number. The reported amount of storage reserved for the process, which is available to expressions on the CommandLineTool as `runtime.tmpdirSize`, must be a non-zero integer. type: - string - number required: [] description: |- Specify basic hardware resource requirements. "min" is the minimum amount of a resource that must be reserved to schedule a job. If "min" cannot be satisfied, the job should not be run. "max" is the maximum amount of a resource that the job shall be allocated. If a node has sufficient resources, multiple jobs may be scheduled on a single node provided each job's "max" resource requirements are met. If a job attempts to exceed its resource allocation, an implementation may deny additional resources, which may result in job failure. If both "min" and "max" are specified, an implementation may choose to allocate any amount between "min" and "max", with the actual allocation provided in the `runtime` object. If "min" is specified but "max" is not, then "max" == "min" If "max" is specified by "min" is not, then "min" == "max". It is an error if max < min. It is an error if the value of any of these fields is negative. If neither "min" nor "max" is specified for a resource, use the default values below. WorkReuseMap: type: object properties: enableReuse: type: - string - boolean required: - enableReuse description: |- For implementations that support reusing output from past work (on the assumption that same code and same input produce same results), control whether to enable or disable the reuse behavior for a particular tool or step (to accommodate situations where that assumption is incorrect). A reused step is not executed but instead returns the same output as the original execution. If `WorkReuse` is not specified, correct tools should assume it is enabled by default. NetworkAccessMap: type: object properties: networkAccess: type: - string - boolean required: - networkAccess description: |- Indicate whether a process requires outgoing IPv4/IPv6 network access. Choice of IPv4 or IPv6 is implementation and site specific, correct tools must support both. If `networkAccess` is false or not specified, tools must not assume network access, except for localhost (the loopback device). If `networkAccess` is true, the tool must be able to make outgoing connections to network resources. Resources may be on a private subnet or the public Internet. However, implementations and sites may apply their own security policies to restrict what is accessible by the tool. Enabling network access does not imply a publicly routable IP address or the ability to accept inbound connections. InplaceUpdateRequirementMap: type: object properties: inplaceUpdate: type: boolean required: - inplaceUpdate description: |2- If `inplaceUpdate` is true, then an implementation supporting this feature may permit tools to directly update files with `writable: true` in InitialWorkDirRequirement. That is, as an optimization, files may be destructively modified in place as opposed to copied and updated. An implementation must ensure that only one workflow step may access a writable file at a time. It is an error if a file which is writable by one workflow step file is accessed (for reading or writing) by any other workflow step running independently. However, a file which has been updated in a previous completed step may be used as input to multiple steps, provided it is read-only in every step. Workflow steps which modify a file must produce the modified file as output. Downstream steps which further process the file must use the output of previous steps, and not refer to a common input (this is necessary for both ordering and correctness). Workflow authors should provide this in the `hints` section. The intent of this feature is that workflows produce the same results whether or not InplaceUpdateRequirement is supported by the implementation, and this feature is primarily available as an optimization for particular environments. Users and implementers should be aware that workflows that destructively modify inputs may not be repeatable or reproducible. In particular, enabling this feature implies that WorkReuse should not be enabled. ToolTimeLimitMap: type: object properties: timelimit: description: |- The time limit, in seconds. A time limit of zero means no time limit. Negative time limits are an error. type: - string - number required: - timelimit description: |- Set an upper limit on the execution time of a CommandLineTool. A CommandLineTool whose execution duration exceeds the time limit may be preemptively terminated and considered failed. May also be used by batch systems to make scheduling decisions. The execution duration excludes external operations, such as staging of files, pulling a docker image etc, and only counts wall-time for the execution of the command line itself. SubworkflowFeatureRequirementMap: type: object properties: {} required: [] description: |- Indicates that the workflow platform must support nested workflows in the `run` field of [WorkflowStep](#WorkflowStep). ScatterFeatureRequirementMap: type: object properties: {} required: [] description: |- Indicates that the workflow platform must support the `scatter` and `scatterMethod` fields of [WorkflowStep](#WorkflowStep). MultipleInputFeatureRequirementMap: type: object properties: {} required: [] description: |- Indicates that the workflow platform must support multiple inbound data links listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput). StepInputExpressionRequirementMap: type: object properties: {} required: [] description: |- Indicate that the workflow platform must support the `valueFrom` field of [WorkflowStepInput](#WorkflowStepInput). CWLFile: type: object allOf: - oneOf: - $ref: '#/definitions/Workflow' - $ref: '#/definitions/CommandLineTool' - $ref: '#/definitions/ExpressionTool' - oneOf: - $ref: '#/definitions/CWLDocumentMetadata' properties: $schemas: true id: true stderr: true successCodes: true cwlVersion: true outputs: true label: true stdout: true requirements: true doc: true temporaryFailCodes: true expression: true hints: true arguments: true stdin: true baseCommand: true class: true permanentFailCodes: true $namespaces: true steps: true inputs: true intent: true patternProperties: ^\w+:.*$: type: object ^\w+:\/\/.*: type: object additionalProperties: false CWLGraph: type: object properties: $graph: type: array items: $ref: '#/definitions/CWLFile' cwlVersion: description: |- CWL document version. Always required at the document root. Not required for a Process embedded inside another Process. enum: - draft-2 - draft-3 - draft-3.dev1 - draft-3.dev2 - draft-3.dev3 - draft-3.dev4 - draft-3.dev5 - draft-4.dev1 - draft-4.dev2 - draft-4.dev3 - v1.0 - v1.0.dev4 - v1.1 - v1.1.0-dev1 - v1.2 - v1.2.0-dev1 - v1.2.0-dev2 - v1.2.0-dev3 - v1.2.0-dev4 - v1.2.0-dev5 type: string required: - $graph CWLGraphOrFile: type: object additionalProperties: false allOf: - oneOf: - $ref: '#/definitions/CWLGraph' - $ref: '#/definitions/CWLFile' - $ref: '#/definitions/CWLDocumentMetadata' properties: $schemas: true id: true stderr: true successCodes: true cwlVersion: true outputs: true label: true stdout: true requirements: true doc: true temporaryFailCodes: true expression: true hints: true $graph: true arguments: true stdin: true baseCommand: true class: true permanentFailCodes: true $namespaces: true steps: true inputs: true intent: true patternProperties: ^\w+:.*$: type: object ^\w+:\/\/.*: type: object