{ "description": "A workflow describes a set of **steps** and the **dependencies** between\n\nthose processes. When a process produces output that will be consumed by a\n\nsecond process, the first process is a dependency of the second process.\n\n\n\nWhen there is a dependency, the workflow engine must execute the preceeding\n\nprocess and wait for it to successfully produce output before executing the\n\ndependent process. If two processes are defined in the workflow graph that\n\nare not directly or indirectly dependent, these processes are\n\n**independent**, and may execute in any order or execute concurrently. A\n\nworkflow is complete when all steps have been executed.\n\n\n\nDependencies between parameters are expressed using the `source` field on\n\n[workflow step input parameters](#WorkflowStepInput) and [workflow output\n\nparameters](#WorkflowOutputParameter).\n\n\n\nThe `source` field expresses the dependency of one parameter on another\n\nsuch that when a value is associated with the parameter specified by\n\n`source`, that value is propagated to the destination parameter. When all\n\ndata links inbound to a given step are fufilled, the step is ready to\n\nexecute.\n\n\n\n## Workflow success and failure\n\n\n\nA completed process must result in one of `success`, `temporaryFailure` or\n\n`permanentFailure` states. An implementation may choose to retry a process\n\nexecution which resulted in `temporaryFailure`. An implementation may\n\nchoose to either continue running other steps of a workflow, or terminate\n\nimmediately upon `permanentFailure`.\n\n\n\n* If any step of a workflow execution results in `permanentFailure`, then the\n\nworkflow status is `permanentFailure`.\n\n\n\n* If one or more steps result in `temporaryFailure` and all other steps\n\ncomplete `success` or are not executed, then the workflow status is\n\n`temporaryFailure`.\n\n\n\n* If all workflow steps are executed and complete with `success`, then the workflow\n\nstatus is `success`.\n\n\n\n# Extensions\n\n\n\n[ScatterFeatureRequirement](#ScatterFeatureRequirement) and\n\n[SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) are\n\navailable as standard extensions to core workflow semantics.", "type": "object", "properties": { "class": { "type": "string" }, "steps": { "description": "The individual steps that make up the workflow. Each step is executed when all of its\n\ninput data links are fufilled. An implementation may choose to execute\n\nthe steps in a different order than listed and/or execute steps\n\nconcurrently, provided that dependencies between steps are met.", "type": "array", "items": { "$ref": "#/definitions/WorkflowStep" } }, "outputs": { "description": "Defines the parameters representing the output of the process. May be\n\nused to generate and/or validate the output object.", "type": "array", "items": { "$ref": "#/definitions/WorkflowOutputParameter" } }, "id": { "description": "The unique identifier for this process object.", "type": "string" }, "inputs": { "description": "Defines the input parameters of the process. The process is ready to\n\nrun when all required input parameters are associated with concrete\n\nvalues. Input parameters include a schema for each parameter which is\n\nused to validate the input object. It may also be used to build a user\n\ninterface for constructing the input object.", "type": "array", "items": { "$ref": "#/definitions/InputParameter" } }, "requirements": { "description": "Declares requirements that apply to either the runtime environment or the\n\nworkflow engine that must be met in order to execute this process. If\n\nan implementation cannot satisfy all requirements, or a requirement is\n\nlisted which is not recognized by the implementation, it is a fatal\n\nerror and the implementation must not attempt to run the process,\n\nunless overridden at user option.", "type": "array", "items": { "$ref": "#/definitions/ProcessRequirement" } }, "hints": { "description": "Declares hints applying to either the runtime environment or the\n\nworkflow engine that may be helpful in executing this process. It is\n\nnot an error if an implementation cannot satisfy all hints, however\n\nthe implementation may report a warning.", "type": "array", "items": {} }, "label": { "description": "A short, human-readable label of this process object.", "type": "string" }, "description": { "description": "A long, human-readable description of this process object.", "type": "string" }, "cwlVersion": { "$ref": "#/definitions/CWLVersions", "description": "CWL document version" } }, "required": [ "class", "steps", "outputs", "inputs" ], "definitions": { "WorkflowStep": { "description": "A workflow step is an executable element of a workflow. It specifies the\n\nunderlying process implementation (such as `CommandLineTool`) in the `run`\n\nfield and connects the input and output parameters of the underlying\n\nprocess to workflow parameters.\n\n\n\n# Scatter/gather\n\n\n\nTo use scatter/gather,\n\n[ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified\n\nin the workflow or workflow step requirements.\n\n\n\nA \"scatter\" operation specifies that the associated workflow step or\n\nsubworkflow should execute separately over a list of input elements. Each\n\njob making up a scatter operation is independent and may be executed\n\nconcurrently.\n\n\n\nThe `scatter` field specifies one or more input parameters which will be\n\nscattered. An input parameter may be listed more than once. The declared\n\ntype of each input parameter is implicitly wrapped in an array for each\n\ntime it appears in the `scatter` field. As a result, upstream parameters\n\nwhich are connected to scattered parameters may be arrays.\n\n\n\nAll output parameter types are also implicitly wrapped in arrays. Each job\n\nin the scatter results in an entry in the output array.\n\n\n\nIf `scatter` declares more than one input parameter, `scatterMethod`\n\ndescribes how to decompose the input into a discrete set of jobs.\n\n\n\n* **dotproduct** specifies that each of the input arrays are aligned and one\n\nelement taken from each array to construct each job. It is an error\n\nif all input arrays are not the same length.\n\n\n\n* **nested_crossproduct** specifies the Cartesian product of the inputs,\n\nproducing a job for every combination of the scattered inputs. The\n\noutput must be nested arrays for each level of scattering, in the\n\norder that the input arrays are listed in the `scatter` field.\n\n\n\n* **flat_crossproduct** specifies the Cartesian product of the inputs,\n\nproducing a job for every combination of the scattered inputs. The\n\noutput arrays must be flattened to a single level, but otherwise listed in the\n\norder that the input arrays are listed in the `scatter` field.\n\n\n\n# Subworkflows\n\n\n\nTo specify a nested workflow as part of a workflow step,\n\n[SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) must be\n\nspecified in the workflow or workflow step requirements.", "type": "object", "properties": { "id": { "description": "The unique identifier for this workflow step.", "type": "string" }, "inputs": { "description": "Defines the input parameters of the workflow step. The process is ready to\n\nrun when all required input parameters are associated with concrete\n\nvalues. Input parameters include a schema for each parameter which is\n\nused to validate the input object. It may also be used build a user\n\ninterface for constructing the input object.", "type": "array", "items": { "$ref": "#/definitions/WorkflowStepInput" } }, "outputs": { "description": "Defines the parameters representing the output of the process. May be\n\nused to generate and/or validate the output object.", "type": "array", "items": { "$ref": "#/definitions/WorkflowStepOutput" } }, "requirements": { "description": "Declares requirements that apply to either the runtime environment or the\n\nworkflow engine that must be met in order to execute this workflow step. If\n\nan implementation cannot satisfy all requirements, or a requirement is\n\nlisted which is not recognized by the implementation, it is a fatal\n\nerror and the implementation must not attempt to run the process,\n\nunless overridden at user option.", "type": "array", "items": { "$ref": "#/definitions/ProcessRequirement" } }, "hints": { "description": "Declares hints applying to either the runtime environment or the\n\nworkflow engine that may be helpful in executing this workflow step. It is\n\nnot an error if an implementation cannot satisfy all hints, however\n\nthe implementation may report a warning.", "type": "array", "items": {} }, "label": { "description": "A short, human-readable label of this process object.", "type": "string" }, "description": { "description": "A long, human-readable description of this process object.", "type": "string" }, "run": { "description": "Specifies the process to run.", "anyOf": [ { "type": "string" }, { "$ref": "#/definitions/Process" } ] }, "scatter": { "anyOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } } ] }, "scatterMethod": { "$ref": "#/definitions/ScatterMethod", "description": "Required if `scatter` is an array of more than one element." } }, "required": [ "id", "inputs", "outputs", "run" ] }, "WorkflowStepInput": { "description": "The input of a workflow step connects an upstream parameter (from the\n\nworkflow inputs, or the outputs of other workflows steps) with the input\n\nparameters of the underlying process.\n\n\n\n## Input object\n\n\n\nA WorkflowStepInput object must contain an `id` field in the form\n\n`#fieldname` or `#stepname.fieldname`. When the `id` field contains a\n\nperiod `.` the field name consists of the characters following the final\n\nperiod. This defines a field of the workflow step input object with the\n\nvalue of the `source` parameter(s).\n\n\n\n## Merging\n\n\n\nTo merge multiple inbound data links,\n\n[MultipleInputFeatureRequirement](#MultipleInputFeatureRequirement) must be specified\n\nin the workflow or workflow step requirements.\n\n\n\nIf the sink parameter is an array, or named in a [workflow\n\nscatter](#WorkflowStep) operation, there may be multiple inbound data links\n\nlisted in the `source` field. The values from the input links are merged\n\ndepending on the method specified in the `linkMerge` field. If not\n\nspecified, the default method is \"merge_nested\".\n\n\n\n* **merge_nested**\n\n\n\nThe input must be an array consisting of exactly one entry for each\n\ninput link. If \"merge_nested\" is specified with a single link, the value\n\nfrom the link must be wrapped in a single-item list.\n\n\n\n* **merge_flattened**\n\n\n\n1. The source and sink parameters must be compatible types, or the source\n\ntype must be compatible with single element from the \"items\" type of\n\nthe destination array parameter.\n\n2. Source parameters which are arrays are concatenated.\n\nSource parameters which are single element types are appended as\n\nsingle elements.", "type": "object", "properties": { "id": { "description": "A unique identifier for this workflow input parameter.", "type": "string" }, "default": { "description": "The default value for this parameter if there is no `source`\n\nfield." }, "valueFrom": { "description": "To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must\n\nbe specified in the workflow or workflow step requirements.\n\n\n\nIf `valueFrom` is a constant string value, use this as the value for\n\nthis input parameter.\n\n\n\nIf `valueFrom` is a parameter reference or expression, it must be\n\nevaluated to yield the actual value to be assiged to the input field.\n\n\n\nThe `self` value of in the parameter reference or expression must be\n\nthe value of the parameter(s) specified in the `source` field, or\n\nnull if there is no `source` field.\n\n\n\nThe value of `inputs` in the parameter reference or expression is the\n\ninput object to the workflow step after assigning the `source` values,\n\nbut before evaluating any step with `valueFrom`. The order of\n\nevaluating `valueFrom` among step input parameters is undefined.", "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] }, "source": { "description": "Specifies one or more workflow parameters that will provide input to\n\nthe underlying process parameter.", "anyOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } } ] }, "linkMerge": { "$ref": "#/definitions/LinkMergeMethod", "description": "The method to use to merge multiple inbound links into a single array.\n\nIf not specified, the default method is \"merge_nested\"." } }, "required": [ "id" ] }, "LinkMergeMethod": { "type": "string", "enum": [ "merge_nested", "merge_flattened" ] }, "WorkflowStepOutput": { "description": "Associate an output parameter of the underlying process with a workflow\n\nparameter. The workflow parameter (given in the `id` field) be may be used\n\nas a `source` to connect with input parameters of other workflow steps, or\n\nwith an output parameter of the process.", "type": "object", "properties": { "id": { "description": "A unique identifier for this workflow output parameter. This is the\n\nidentifier to use in the `source` field of `WorkflowStepInput` to\n\nconnect the output value to downstream parameters.", "type": "string" } }, "required": [ "id" ] }, "ProcessRequirement": { "description": "A process requirement declares a prerequisite that may or must be fulfilled\n\nbefore executing a process. See [`Process.hints`](#process) and\n\n[`Process.requirements`](#process).\n\n\n\nProcess requirements are the primary mechanism for specifying extensions to\n\nthe CWL core specification.", "type": "object", "properties": { "class": { "description": "The specific requirement type.", "type": "string" } }, "required": [ "class" ] }, "Process": { "description": "The base executable type in CWL is the `Process` object defined by the\n\ndocument. Note that the `Process` object is abstract and cannot be\n\ndirectly executed.", "type": "object", "properties": { "id": { "description": "The unique identifier for this process object.", "type": "string" }, "inputs": { "description": "Defines the input parameters of the process. The process is ready to\n\nrun when all required input parameters are associated with concrete\n\nvalues. Input parameters include a schema for each parameter which is\n\nused to validate the input object. It may also be used to build a user\n\ninterface for constructing the input object.", "type": "array", "items": { "$ref": "#/definitions/InputParameter" } }, "outputs": { "description": "Defines the parameters representing the output of the process. May be\n\nused to generate and/or validate the output object.", "type": "array", "items": { "$ref": "#/definitions/OutputParameter" } }, "requirements": { "description": "Declares requirements that apply to either the runtime environment or the\n\nworkflow engine that must be met in order to execute this process. If\n\nan implementation cannot satisfy all requirements, or a requirement is\n\nlisted which is not recognized by the implementation, it is a fatal\n\nerror and the implementation must not attempt to run the process,\n\nunless overridden at user option.", "type": "array", "items": { "$ref": "#/definitions/ProcessRequirement" } }, "hints": { "description": "Declares hints applying to either the runtime environment or the\n\nworkflow engine that may be helpful in executing this process. It is\n\nnot an error if an implementation cannot satisfy all hints, however\n\nthe implementation may report a warning.", "type": "array", "items": {} }, "label": { "description": "A short, human-readable label of this process object.", "type": "string" }, "description": { "description": "A long, human-readable description of this process object.", "type": "string" }, "cwlVersion": { "$ref": "#/definitions/CWLVersions", "description": "CWL document version" } }, "required": [ "inputs", "outputs" ] }, "InputParameter": { "type": "object", "properties": { "id": { "description": "The unique identifier for this parameter object.", "type": "string" }, "inputBinding": { "$ref": "#/definitions/InputBinding", "description": "Describes how to handle the inputs of a process and convert them\n\ninto a concrete form for execution, such as command line parameters." }, "default": { "description": "The default value for this parameter if not provided in the input\n\nobject." }, "type": { "description": "Specify valid types of data that may be assigned to this parameter.", "anyOf": [ { "type": "string", "enum": [ "File" ] }, { "type": "string", "enum": [ "null" ] }, { "type": "string", "enum": [ "boolean" ] }, { "type": "string", "enum": [ "int" ] }, { "type": "string", "enum": [ "long" ] }, { "type": "string", "enum": [ "float" ] }, { "type": "string", "enum": [ "double" ] }, { "type": "string", "enum": [ "string" ] }, { "$ref": "#/definitions/InputRecordSchema" }, { "$ref": "#/definitions/InputEnumSchema" }, { "$ref": "#/definitions/InputArraySchema" }, { "type": "string" }, { "type": "array", "items": { "anyOf": [ { "type": "string", "enum": [ "File" ] }, { "type": "string", "enum": [ "null" ] }, { "type": "string", "enum": [ "boolean" ] }, { "type": "string", "enum": [ "int" ] }, { "type": "string", "enum": [ "long" ] }, { "type": "string", "enum": [ "float" ] }, { "type": "string", "enum": [ "double" ] }, { "type": "string", "enum": [ "string" ] }, { "$ref": "#/definitions/InputRecordSchema" }, { "$ref": "#/definitions/InputEnumSchema" }, { "$ref": "#/definitions/InputArraySchema" }, { "type": "string" } ] } } ] }, "label": { "description": "A short, human-readable label of this parameter object.", "type": "string" }, "description": { "description": "A long, human-readable description of this parameter object.", "type": "string" }, "secondaryFiles": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nDescribes files that must be included alongside the primary file(s).\n\n\n\nIf the value is an expression, the value of `self` in the expression\n\nmust be the primary input or output File to which this binding applies.\n\n\n\nIf the value is a string, it specifies that the following pattern\n\nshould be applied to the primary file:\n\n\n\n1. If string begins with one or more caret `^` characters, for each\n\ncaret, remove the last file extension from the path (the last\n\nperiod `.` and all following characters). If there are no file\n\nextensions, the path is unchanged.\n\n2. Append the remainder of the string to the end of the file path.", "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] }, { "type": "array", "items": { "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] } } ] }, "format": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nFor input parameters, this must be one or more URIs of a concept nodes\n\nthat represents file formats which are allowed as input to this\n\nparameter, preferrably defined within an ontology. If no ontology is\n\navailable, file formats may be tested by exact match.\n\n\n\nFor output parameters, this is the file format that will be assigned to\n\nthe output parameter.", "anyOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] }, "streamable": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nA value of `true` indicates that the file is read or written\n\nsequentially without seeking. An implementation may use this flag to\n\nindicate whether it is valid to stream file contents using a named\n\npipe. Default: `false`.", "type": "boolean" } }, "required": [ "id" ] }, "InputBinding": { "type": "object", "properties": { "loadContents": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nRead up to the first 64 KiB of text from the file and place it in the\n\n\"contents\" field of the file object for use by expressions.", "type": "boolean" } } }, "InputRecordSchema": { "type": "object", "properties": { "fields": { "description": "Defines the fields of the record.", "type": "array", "items": { "$ref": "#/definitions/InputRecordField" } }, "type": { "description": "Must be `record`", "type": "string", "enum": [ "record" ] }, "secondaryFiles": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nDescribes files that must be included alongside the primary file(s).\n\n\n\nIf the value is an expression, the value of `self` in the expression\n\nmust be the primary input or output File to which this binding applies.\n\n\n\nIf the value is a string, it specifies that the following pattern\n\nshould be applied to the primary file:\n\n\n\n1. If string begins with one or more caret `^` characters, for each\n\ncaret, remove the last file extension from the path (the last\n\nperiod `.` and all following characters). If there are no file\n\nextensions, the path is unchanged.\n\n2. Append the remainder of the string to the end of the file path.", "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] }, { "type": "array", "items": { "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] } } ] }, "format": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nFor input parameters, this must be one or more URIs of a concept nodes\n\nthat represents file formats which are allowed as input to this\n\nparameter, preferrably defined within an ontology. If no ontology is\n\navailable, file formats may be tested by exact match.\n\n\n\nFor output parameters, this is the file format that will be assigned to\n\nthe output parameter.", "anyOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] }, "streamable": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nA value of `true` indicates that the file is read or written\n\nsequentially without seeking. An implementation may use this flag to\n\nindicate whether it is valid to stream file contents using a named\n\npipe. Default: `false`.", "type": "boolean" } }, "required": [ "type" ] }, "InputRecordField": { "type": "object", "properties": { "inputBinding": { "$ref": "#/definitions/InputBinding" }, "type": { "description": "The field type", "anyOf": [ { "type": "string", "enum": [ "null" ] }, { "type": "string", "enum": [ "boolean" ] }, { "type": "string", "enum": [ "int" ] }, { "type": "string", "enum": [ "long" ] }, { "type": "string", "enum": [ "float" ] }, { "type": "string", "enum": [ "double" ] }, { "type": "string", "enum": [ "string" ] }, { "$ref": "#/definitions/InputRecordSchema" }, { "$ref": "#/definitions/InputEnumSchema" }, { "$ref": "#/definitions/InputArraySchema" }, { "type": "string" }, { "type": "array", "items": { "anyOf": [ { "type": "string", "enum": [ "null" ] }, { "type": "string", "enum": [ "boolean" ] }, { "type": "string", "enum": [ "int" ] }, { "type": "string", "enum": [ "long" ] }, { "type": "string", "enum": [ "float" ] }, { "type": "string", "enum": [ "double" ] }, { "type": "string", "enum": [ "string" ] }, { "$ref": "#/definitions/InputRecordSchema" }, { "$ref": "#/definitions/InputEnumSchema" }, { "$ref": "#/definitions/InputArraySchema" }, { "type": "string" } ] } } ] }, "name": { "description": "The name of the field", "type": "string" }, "doc": { "description": "A documentation string for this field", "type": "string" } }, "required": [ "type", "name" ] }, "InputEnumSchema": { "type": "object", "properties": { "inputBinding": { "$ref": "#/definitions/InputBinding" }, "type": { "description": "Must be `enum`", "type": "string", "enum": [ "enum" ] }, "symbols": { "description": "Defines the set of valid symbols.", "type": "array", "items": { "type": "string" } }, "secondaryFiles": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nDescribes files that must be included alongside the primary file(s).\n\n\n\nIf the value is an expression, the value of `self` in the expression\n\nmust be the primary input or output File to which this binding applies.\n\n\n\nIf the value is a string, it specifies that the following pattern\n\nshould be applied to the primary file:\n\n\n\n1. If string begins with one or more caret `^` characters, for each\n\ncaret, remove the last file extension from the path (the last\n\nperiod `.` and all following characters). If there are no file\n\nextensions, the path is unchanged.\n\n2. Append the remainder of the string to the end of the file path.", "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] }, { "type": "array", "items": { "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] } } ] }, "format": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nFor input parameters, this must be one or more URIs of a concept nodes\n\nthat represents file formats which are allowed as input to this\n\nparameter, preferrably defined within an ontology. If no ontology is\n\navailable, file formats may be tested by exact match.\n\n\n\nFor output parameters, this is the file format that will be assigned to\n\nthe output parameter.", "anyOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] }, "streamable": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nA value of `true` indicates that the file is read or written\n\nsequentially without seeking. An implementation may use this flag to\n\nindicate whether it is valid to stream file contents using a named\n\npipe. Default: `false`.", "type": "boolean" } }, "required": [ "type", "symbols" ] }, "InputArraySchema": { "type": "object", "properties": { "inputBinding": { "$ref": "#/definitions/InputBinding" }, "items": { "description": "Defines the type of the array elements.", "anyOf": [ { "type": "string", "enum": [ "null" ] }, { "type": "string", "enum": [ "boolean" ] }, { "type": "string", "enum": [ "int" ] }, { "type": "string", "enum": [ "long" ] }, { "type": "string", "enum": [ "float" ] }, { "type": "string", "enum": [ "double" ] }, { "type": "string", "enum": [ "string" ] }, { "$ref": "#/definitions/InputRecordSchema" }, { "$ref": "#/definitions/InputEnumSchema" }, { "$ref": "#/definitions/InputArraySchema" }, { "type": "string" }, { "type": "array", "items": { "anyOf": [ { "type": "string", "enum": [ "null" ] }, { "type": "string", "enum": [ "boolean" ] }, { "type": "string", "enum": [ "int" ] }, { "type": "string", "enum": [ "long" ] }, { "type": "string", "enum": [ "float" ] }, { "type": "string", "enum": [ "double" ] }, { "type": "string", "enum": [ "string" ] }, { "$ref": "#/definitions/InputRecordSchema" }, { "$ref": "#/definitions/InputEnumSchema" }, { "$ref": "#/definitions/InputArraySchema" }, { "type": "string" } ] } } ] }, "type": { "description": "Must be `array`", "type": "string", "enum": [ "array" ] }, "secondaryFiles": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nDescribes files that must be included alongside the primary file(s).\n\n\n\nIf the value is an expression, the value of `self` in the expression\n\nmust be the primary input or output File to which this binding applies.\n\n\n\nIf the value is a string, it specifies that the following pattern\n\nshould be applied to the primary file:\n\n\n\n1. If string begins with one or more caret `^` characters, for each\n\ncaret, remove the last file extension from the path (the last\n\nperiod `.` and all following characters). If there are no file\n\nextensions, the path is unchanged.\n\n2. Append the remainder of the string to the end of the file path.", "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] }, { "type": "array", "items": { "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] } } ] }, "format": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nFor input parameters, this must be one or more URIs of a concept nodes\n\nthat represents file formats which are allowed as input to this\n\nparameter, preferrably defined within an ontology. If no ontology is\n\navailable, file formats may be tested by exact match.\n\n\n\nFor output parameters, this is the file format that will be assigned to\n\nthe output parameter.", "anyOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] }, "streamable": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nA value of `true` indicates that the file is read or written\n\nsequentially without seeking. An implementation may use this flag to\n\nindicate whether it is valid to stream file contents using a named\n\npipe. Default: `false`.", "type": "boolean" } }, "required": [ "items", "type" ] }, "OutputParameter": { "type": "object", "properties": { "id": { "description": "The unique identifier for this parameter object.", "type": "string" }, "outputBinding": { "$ref": "#/definitions/OutputBinding", "description": "Describes how to handle the outputs of a process." }, "type": { "description": "Specify valid types of data that may be assigned to this parameter.", "anyOf": [ { "type": "string", "enum": [ "File" ] }, { "type": "string", "enum": [ "null" ] }, { "type": "string", "enum": [ "boolean" ] }, { "type": "string", "enum": [ "int" ] }, { "type": "string", "enum": [ "long" ] }, { "type": "string", "enum": [ "float" ] }, { "type": "string", "enum": [ "double" ] }, { "type": "string", "enum": [ "string" ] }, { "$ref": "#/definitions/OutputRecordSchema" }, { "$ref": "#/definitions/OutputEnumSchema" }, { "$ref": "#/definitions/OutputArraySchema" }, { "type": "string" }, { "type": "array", "items": { "anyOf": [ { "type": "string", "enum": [ "File" ] }, { "type": "string", "enum": [ "null" ] }, { "type": "string", "enum": [ "boolean" ] }, { "type": "string", "enum": [ "int" ] }, { "type": "string", "enum": [ "long" ] }, { "type": "string", "enum": [ "float" ] }, { "type": "string", "enum": [ "double" ] }, { "type": "string", "enum": [ "string" ] }, { "$ref": "#/definitions/OutputRecordSchema" }, { "$ref": "#/definitions/OutputEnumSchema" }, { "$ref": "#/definitions/OutputArraySchema" }, { "type": "string" } ] } } ] }, "label": { "description": "A short, human-readable label of this parameter object.", "type": "string" }, "description": { "description": "A long, human-readable description of this parameter object.", "type": "string" }, "secondaryFiles": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nDescribes files that must be included alongside the primary file(s).\n\n\n\nIf the value is an expression, the value of `self` in the expression\n\nmust be the primary input or output File to which this binding applies.\n\n\n\nIf the value is a string, it specifies that the following pattern\n\nshould be applied to the primary file:\n\n\n\n1. If string begins with one or more caret `^` characters, for each\n\ncaret, remove the last file extension from the path (the last\n\nperiod `.` and all following characters). If there are no file\n\nextensions, the path is unchanged.\n\n2. Append the remainder of the string to the end of the file path.", "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] }, { "type": "array", "items": { "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] } } ] }, "format": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nFor input parameters, this must be one or more URIs of a concept nodes\n\nthat represents file formats which are allowed as input to this\n\nparameter, preferrably defined within an ontology. If no ontology is\n\navailable, file formats may be tested by exact match.\n\n\n\nFor output parameters, this is the file format that will be assigned to\n\nthe output parameter.", "anyOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] }, "streamable": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nA value of `true` indicates that the file is read or written\n\nsequentially without seeking. An implementation may use this flag to\n\nindicate whether it is valid to stream file contents using a named\n\npipe. Default: `false`.", "type": "boolean" } }, "required": [ "id" ] }, "OutputBinding": { "type": "object", "properties": {} }, "OutputRecordSchema": { "type": "object", "properties": { "fields": { "description": "Defines the fields of the record.", "type": "array", "items": { "$ref": "#/definitions/OutputRecordField" } }, "type": { "description": "Must be `record`", "type": "string", "enum": [ "record" ] }, "secondaryFiles": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nDescribes files that must be included alongside the primary file(s).\n\n\n\nIf the value is an expression, the value of `self` in the expression\n\nmust be the primary input or output File to which this binding applies.\n\n\n\nIf the value is a string, it specifies that the following pattern\n\nshould be applied to the primary file:\n\n\n\n1. If string begins with one or more caret `^` characters, for each\n\ncaret, remove the last file extension from the path (the last\n\nperiod `.` and all following characters). If there are no file\n\nextensions, the path is unchanged.\n\n2. Append the remainder of the string to the end of the file path.", "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] }, { "type": "array", "items": { "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] } } ] }, "format": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nFor input parameters, this must be one or more URIs of a concept nodes\n\nthat represents file formats which are allowed as input to this\n\nparameter, preferrably defined within an ontology. If no ontology is\n\navailable, file formats may be tested by exact match.\n\n\n\nFor output parameters, this is the file format that will be assigned to\n\nthe output parameter.", "anyOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] }, "streamable": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nA value of `true` indicates that the file is read or written\n\nsequentially without seeking. An implementation may use this flag to\n\nindicate whether it is valid to stream file contents using a named\n\npipe. Default: `false`.", "type": "boolean" } }, "required": [ "type" ] }, "OutputRecordField": { "type": "object", "properties": { "outputBinding": { "$ref": "#/definitions/OutputBinding" }, "type": { "description": "The field type", "anyOf": [ { "type": "string", "enum": [ "null" ] }, { "type": "string", "enum": [ "boolean" ] }, { "type": "string", "enum": [ "int" ] }, { "type": "string", "enum": [ "long" ] }, { "type": "string", "enum": [ "float" ] }, { "type": "string", "enum": [ "double" ] }, { "type": "string", "enum": [ "string" ] }, { "$ref": "#/definitions/OutputRecordSchema" }, { "$ref": "#/definitions/OutputEnumSchema" }, { "$ref": "#/definitions/OutputArraySchema" }, { "type": "string" }, { "type": "array", "items": { "anyOf": [ { "type": "string", "enum": [ "null" ] }, { "type": "string", "enum": [ "boolean" ] }, { "type": "string", "enum": [ "int" ] }, { "type": "string", "enum": [ "long" ] }, { "type": "string", "enum": [ "float" ] }, { "type": "string", "enum": [ "double" ] }, { "type": "string", "enum": [ "string" ] }, { "$ref": "#/definitions/OutputRecordSchema" }, { "$ref": "#/definitions/OutputEnumSchema" }, { "$ref": "#/definitions/OutputArraySchema" }, { "type": "string" } ] } } ] }, "name": { "description": "The name of the field", "type": "string" }, "doc": { "description": "A documentation string for this field", "type": "string" } }, "required": [ "type", "name" ] }, "OutputEnumSchema": { "type": "object", "properties": { "outputBinding": { "$ref": "#/definitions/OutputBinding" }, "type": { "description": "Must be `enum`", "type": "string", "enum": [ "enum" ] }, "symbols": { "description": "Defines the set of valid symbols.", "type": "array", "items": { "type": "string" } }, "secondaryFiles": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nDescribes files that must be included alongside the primary file(s).\n\n\n\nIf the value is an expression, the value of `self` in the expression\n\nmust be the primary input or output File to which this binding applies.\n\n\n\nIf the value is a string, it specifies that the following pattern\n\nshould be applied to the primary file:\n\n\n\n1. If string begins with one or more caret `^` characters, for each\n\ncaret, remove the last file extension from the path (the last\n\nperiod `.` and all following characters). If there are no file\n\nextensions, the path is unchanged.\n\n2. Append the remainder of the string to the end of the file path.", "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] }, { "type": "array", "items": { "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] } } ] }, "format": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nFor input parameters, this must be one or more URIs of a concept nodes\n\nthat represents file formats which are allowed as input to this\n\nparameter, preferrably defined within an ontology. If no ontology is\n\navailable, file formats may be tested by exact match.\n\n\n\nFor output parameters, this is the file format that will be assigned to\n\nthe output parameter.", "anyOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] }, "streamable": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nA value of `true` indicates that the file is read or written\n\nsequentially without seeking. An implementation may use this flag to\n\nindicate whether it is valid to stream file contents using a named\n\npipe. Default: `false`.", "type": "boolean" } }, "required": [ "type", "symbols" ] }, "OutputArraySchema": { "type": "object", "properties": { "outputBinding": { "$ref": "#/definitions/OutputBinding" }, "items": { "description": "Defines the type of the array elements.", "anyOf": [ { "type": "string", "enum": [ "null" ] }, { "type": "string", "enum": [ "boolean" ] }, { "type": "string", "enum": [ "int" ] }, { "type": "string", "enum": [ "long" ] }, { "type": "string", "enum": [ "float" ] }, { "type": "string", "enum": [ "double" ] }, { "type": "string", "enum": [ "string" ] }, { "$ref": "#/definitions/OutputRecordSchema" }, { "$ref": "#/definitions/OutputEnumSchema" }, { "$ref": "#/definitions/OutputArraySchema" }, { "type": "string" }, { "type": "array", "items": { "anyOf": [ { "type": "string", "enum": [ "null" ] }, { "type": "string", "enum": [ "boolean" ] }, { "type": "string", "enum": [ "int" ] }, { "type": "string", "enum": [ "long" ] }, { "type": "string", "enum": [ "float" ] }, { "type": "string", "enum": [ "double" ] }, { "type": "string", "enum": [ "string" ] }, { "$ref": "#/definitions/OutputRecordSchema" }, { "$ref": "#/definitions/OutputEnumSchema" }, { "$ref": "#/definitions/OutputArraySchema" }, { "type": "string" } ] } } ] }, "type": { "description": "Must be `array`", "type": "string", "enum": [ "array" ] }, "secondaryFiles": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nDescribes files that must be included alongside the primary file(s).\n\n\n\nIf the value is an expression, the value of `self` in the expression\n\nmust be the primary input or output File to which this binding applies.\n\n\n\nIf the value is a string, it specifies that the following pattern\n\nshould be applied to the primary file:\n\n\n\n1. If string begins with one or more caret `^` characters, for each\n\ncaret, remove the last file extension from the path (the last\n\nperiod `.` and all following characters). If there are no file\n\nextensions, the path is unchanged.\n\n2. Append the remainder of the string to the end of the file path.", "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] }, { "type": "array", "items": { "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] } } ] }, "format": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nFor input parameters, this must be one or more URIs of a concept nodes\n\nthat represents file formats which are allowed as input to this\n\nparameter, preferrably defined within an ontology. If no ontology is\n\navailable, file formats may be tested by exact match.\n\n\n\nFor output parameters, this is the file format that will be assigned to\n\nthe output parameter.", "anyOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] }, "streamable": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nA value of `true` indicates that the file is read or written\n\nsequentially without seeking. An implementation may use this flag to\n\nindicate whether it is valid to stream file contents using a named\n\npipe. Default: `false`.", "type": "boolean" } }, "required": [ "items", "type" ] }, "CWLVersions": { "type": "string", "enum": [ "draft-3" ] }, "ScatterMethod": { "type": "string", "enum": [ "dotproduct", "nested_crossproduct", "flat_crossproduct" ] }, "WorkflowOutputParameter": { "description": "Describe an output parameter of a workflow. The parameter must be\n\nconnected to one or more parameters defined in the workflow that will\n\nprovide the value of the output parameter.", "type": "object", "properties": { "id": { "description": "The unique identifier for this parameter object.", "type": "string" }, "outputBinding": { "$ref": "#/definitions/OutputBinding", "description": "Describes how to handle the outputs of a process." }, "type": { "description": "Specify valid types of data that may be assigned to this parameter.", "anyOf": [ { "type": "string", "enum": [ "File" ] }, { "type": "string", "enum": [ "null" ] }, { "type": "string", "enum": [ "boolean" ] }, { "type": "string", "enum": [ "int" ] }, { "type": "string", "enum": [ "long" ] }, { "type": "string", "enum": [ "float" ] }, { "type": "string", "enum": [ "double" ] }, { "type": "string", "enum": [ "string" ] }, { "$ref": "#/definitions/OutputRecordSchema" }, { "$ref": "#/definitions/OutputEnumSchema" }, { "$ref": "#/definitions/OutputArraySchema" }, { "type": "string" }, { "type": "array", "items": { "anyOf": [ { "type": "string", "enum": [ "File" ] }, { "type": "string", "enum": [ "null" ] }, { "type": "string", "enum": [ "boolean" ] }, { "type": "string", "enum": [ "int" ] }, { "type": "string", "enum": [ "long" ] }, { "type": "string", "enum": [ "float" ] }, { "type": "string", "enum": [ "double" ] }, { "type": "string", "enum": [ "string" ] }, { "$ref": "#/definitions/OutputRecordSchema" }, { "$ref": "#/definitions/OutputEnumSchema" }, { "$ref": "#/definitions/OutputArraySchema" }, { "type": "string" } ] } } ] }, "label": { "description": "A short, human-readable label of this parameter object.", "type": "string" }, "description": { "description": "A long, human-readable description of this parameter object.", "type": "string" }, "secondaryFiles": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nDescribes files that must be included alongside the primary file(s).\n\n\n\nIf the value is an expression, the value of `self` in the expression\n\nmust be the primary input or output File to which this binding applies.\n\n\n\nIf the value is a string, it specifies that the following pattern\n\nshould be applied to the primary file:\n\n\n\n1. If string begins with one or more caret `^` characters, for each\n\ncaret, remove the last file extension from the path (the last\n\nperiod `.` and all following characters). If there are no file\n\nextensions, the path is unchanged.\n\n2. Append the remainder of the string to the end of the file path.", "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] }, { "type": "array", "items": { "anyOf": [ { "type": "string" }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] } } ] }, "format": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nFor input parameters, this must be one or more URIs of a concept nodes\n\nthat represents file formats which are allowed as input to this\n\nparameter, preferrably defined within an ontology. If no ontology is\n\navailable, file formats may be tested by exact match.\n\n\n\nFor output parameters, this is the file format that will be assigned to\n\nthe output parameter.", "anyOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } }, { "type": "string", "enum": [ "ExpressionPlaceholder" ] } ] }, "streamable": { "description": "Only valid when `type: File` or is an array of `items: File`.\n\n\n\nA value of `true` indicates that the file is read or written\n\nsequentially without seeking. An implementation may use this flag to\n\nindicate whether it is valid to stream file contents using a named\n\npipe. Default: `false`.", "type": "boolean" }, "source": { "description": "Specifies one or more workflow parameters that will provide input to\n\nthe underlying process parameter.", "anyOf": [ { "type": "string" }, { "type": "array", "items": { "type": "string" } } ] }, "linkMerge": { "$ref": "#/definitions/LinkMergeMethod", "description": "The method to use to merge multiple inbound links into a single array.\n\nIf not specified, the default method is \"merge_nested\"." } }, "required": [ "id" ] } }, "$schema": "http://json-schema.org/draft-04/schema#" }