diff --git a/cwltool/schemas/v1.0/CommandLineTool.yml b/cwltool/schemas/v1.0/CommandLineTool.yml index 747cecb27..805f0a0ba 100644 --- a/cwltool/schemas/v1.0/CommandLineTool.yml +++ b/cwltool/schemas/v1.0/CommandLineTool.yml @@ -94,16 +94,16 @@ $graph: 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. fields: - - name: "envName" - type: "string" + - name: envName + type: string doc: The environment variable name - - name: "envValue" - type: ["string", "#Expression"] + - name: envValue + type: [string, Expression] doc: The environment variable value - type: record name: CommandLineBinding - extends: "#InputBinding" + extends: InputBinding doc: | When listed under `inputBinding` in the input schema, the term @@ -138,28 +138,28 @@ $graph: - **null**: Add nothing. fields: - - name: "position" - type: ["null", "int"] + - name: position + type: int? doc: "The sorting key. Default position is 0." - - name: "prefix" - type: [ "null", "string"] + - name: prefix + type: string? doc: "Command line prefix to add before the value." - - name: "separate" - type: ["null", boolean] + - name: separate + type: boolean? doc: | 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. - - name: "itemSeparator" - type: ["null", "string"] + - name: itemSeparator + type: string? doc: | Join the array elements into a single string with the elements separated by by `itemSeparator`. - - name: "valueFrom" + - name: valueFrom type: - "null" - - "string" - - "#Expression" + - string + - Expression jsonldPredicate: "cwl:valueFrom" doc: | If `valueFrom` is a constant string value, use this as the value and @@ -174,7 +174,7 @@ $graph: When a binding is part of the `CommandLineTool.arguments` field, the `valueFrom` field is required. - name: shellQuote - type: ["null", boolean] + type: boolean? doc: | If `ShellCommandRequirement` is in the requirements for the current command, this controls whether the value is quoted on the command line (default is true). @@ -182,7 +182,7 @@ $graph: - type: record name: CommandOutputBinding - extends: "#OutputBinding" + extends: OutputBinding doc: | Describes how to generate an output parameter based on the files produced by a CommandLineTool. @@ -198,7 +198,7 @@ $graph: type: - "null" - string - - "#Expression" + - Expression - type: array items: string doc: | @@ -221,7 +221,7 @@ $graph: type: - "null" - string - - "#Expression" + - Expression doc: | Evaluate an expression to generate the output value. If `glob` was specified, the value of `self` must be an array containing file objects @@ -234,136 +234,136 @@ $graph: - name: CommandInputRecordField type: record - extends: "#InputRecordField" + extends: InputRecordField specialize: - - specializeFrom: "#InputRecordSchema" - specializeTo: "#CommandInputRecordSchema" - - specializeFrom: "#InputEnumSchema" - specializeTo: "#CommandInputEnumSchema" - - specializeFrom: "#InputArraySchema" - specializeTo: "#CommandInputArraySchema" - - specializeFrom: "#InputBinding" - specializeTo: "#CommandLineBinding" + - specializeFrom: InputRecordSchema + specializeTo: CommandInputRecordSchema + - specializeFrom: InputEnumSchema + specializeTo: CommandInputEnumSchema + - specializeFrom: InputArraySchema + specializeTo: CommandInputArraySchema + - specializeFrom: InputBinding + specializeTo: CommandLineBinding - name: CommandInputRecordSchema type: record - extends: "#InputRecordSchema" + extends: InputRecordSchema specialize: - - specializeFrom: "#InputRecordField" - specializeTo: "#CommandInputRecordField" + - specializeFrom: InputRecordField + specializeTo: CommandInputRecordField - name: CommandInputEnumSchema type: record - extends: "#InputEnumSchema" + extends: InputEnumSchema specialize: - - specializeFrom: "#InputBinding" - specializeTo: "#CommandLineBinding" + - specializeFrom: InputBinding + specializeTo: CommandLineBinding - name: CommandInputArraySchema type: record - extends: "#InputArraySchema" + extends: InputArraySchema specialize: - - specializeFrom: "#InputRecordSchema" - specializeTo: "#CommandInputRecordSchema" - - specializeFrom: "#InputEnumSchema" - specializeTo: "#CommandInputEnumSchema" - - specializeFrom: "#InputArraySchema" - specializeTo: "#CommandInputArraySchema" - - specializeFrom: "#InputBinding" - specializeTo: "#CommandLineBinding" + - specializeFrom: InputRecordSchema + specializeTo: CommandInputRecordSchema + - specializeFrom: InputEnumSchema + specializeTo: CommandInputEnumSchema + - specializeFrom: InputArraySchema + specializeTo: CommandInputArraySchema + - specializeFrom: InputBinding + specializeTo: CommandLineBinding - name: CommandOutputRecordField type: record - extends: "#OutputRecordField" + extends: OutputRecordField specialize: - - specializeFrom: "#OutputRecordSchema" - specializeTo: "#CommandOutputRecordSchema" - - specializeFrom: "#OutputEnumSchema" - specializeTo: "#CommandOutputEnumSchema" - - specializeFrom: "#OutputArraySchema" - specializeTo: "#CommandOutputArraySchema" - - specializeFrom: "#OutputBinding" - specializeTo: "#CommandOutputBinding" + - specializeFrom: OutputRecordSchema + specializeTo: CommandOutputRecordSchema + - specializeFrom: OutputEnumSchema + specializeTo: CommandOutputEnumSchema + - specializeFrom: OutputArraySchema + specializeTo: CommandOutputArraySchema + - specializeFrom: OutputBinding + specializeTo: CommandOutputBinding - name: CommandOutputRecordSchema type: record - extends: "#OutputRecordSchema" + extends: OutputRecordSchema specialize: - - specializeFrom: "#OutputRecordField" - specializeTo: "#CommandOutputRecordField" + - specializeFrom: OutputRecordField + specializeTo: CommandOutputRecordField - name: CommandOutputEnumSchema type: record - extends: "#OutputEnumSchema" + extends: OutputEnumSchema specialize: - - specializeFrom: "#OutputRecordSchema" - specializeTo: "#CommandOutputRecordSchema" - - specializeFrom: "#OutputEnumSchema" - specializeTo: "#CommandOutputEnumSchema" - - specializeFrom: "#OutputArraySchema" - specializeTo: "#CommandOutputArraySchema" - - specializeFrom: "#OutputBinding" - specializeTo: "#CommandOutputBinding" + - specializeFrom: OutputRecordSchema + specializeTo: CommandOutputRecordSchema + - specializeFrom: OutputEnumSchema + specializeTo: CommandOutputEnumSchema + - specializeFrom: OutputArraySchema + specializeTo: CommandOutputArraySchema + - specializeFrom: OutputBinding + specializeTo: CommandOutputBinding - name: CommandOutputArraySchema type: record - extends: "#OutputArraySchema" + extends: OutputArraySchema specialize: - - specializeFrom: "#OutputRecordSchema" - specializeTo: "#CommandOutputRecordSchema" - - specializeFrom: "#OutputEnumSchema" - specializeTo: "#CommandOutputEnumSchema" - - specializeFrom: "#OutputArraySchema" - specializeTo: "#CommandOutputArraySchema" - - specializeFrom: "#OutputBinding" - specializeTo: "#CommandOutputBinding" + - specializeFrom: OutputRecordSchema + specializeTo: CommandOutputRecordSchema + - specializeFrom: OutputEnumSchema + specializeTo: CommandOutputEnumSchema + - specializeFrom: OutputArraySchema + specializeTo: CommandOutputArraySchema + - specializeFrom: OutputBinding + specializeTo: CommandOutputBinding - type: record name: CommandInputParameter - extends: "#InputParameter" + extends: InputParameter doc: An input parameter for a CommandLineTool. specialize: - - specializeFrom: "#InputRecordSchema" - specializeTo: "#CommandInputRecordSchema" - - specializeFrom: "#InputEnumSchema" - specializeTo: "#CommandInputEnumSchema" - - specializeFrom: "#InputArraySchema" - specializeTo: "#CommandInputArraySchema" - - specializeFrom: "#InputBinding" - specializeTo: "#CommandLineBinding" + - specializeFrom: InputRecordSchema + specializeTo: CommandInputRecordSchema + - specializeFrom: InputEnumSchema + specializeTo: CommandInputEnumSchema + - specializeFrom: InputArraySchema + specializeTo: CommandInputArraySchema + - specializeFrom: InputBinding + specializeTo: CommandLineBinding - type: record name: CommandOutputParameter - extends: "#OutputParameter" + extends: OutputParameter doc: An output parameter for a CommandLineTool. specialize: - - specializeFrom: "#OutputBinding" - specializeTo: "#CommandOutputBinding" + - specializeFrom: OutputBinding + specializeTo: CommandOutputBinding fields: - name: type type: - "null" - - "#CWLType" - - "#stdout" - - "#stderr" - - "#CommandOutputRecordSchema" - - "#CommandOutputEnumSchema" - - "#CommandOutputArraySchema" + - CWLType + - stdout + - stderr + - CommandOutputRecordSchema + - CommandOutputEnumSchema + - CommandOutputArraySchema - string - type: array items: - - "#CWLType" - - "#CommandOutputRecordSchema" - - "#CommandOutputEnumSchema" - - "#CommandOutputArraySchema" + - CWLType + - CommandOutputRecordSchema + - CommandOutputEnumSchema + - CommandOutputArraySchema - string jsonldPredicate: "_id": "sld:type" @@ -471,18 +471,18 @@ $graph: - type: record name: CommandLineTool - extends: "#Process" + extends: Process documentRoot: true specialize: - - specializeFrom: "#InputParameter" - specializeTo: "#CommandInputParameter" - - specializeFrom: "#OutputParameter" - specializeTo: "#CommandOutputParameter" + - specializeFrom: InputParameter + specializeTo: CommandInputParameter + - specializeFrom: OutputParameter + specializeTo: CommandOutputParameter doc: | This defines the schema of the CWL Command Line Tool Description document. fields: - - name: "class" + - name: class jsonldPredicate: "_id": "@type" "_type": "@vocab" @@ -510,17 +510,17 @@ $graph: type: - "null" - type: array - items: [string, "#Expression", "#CommandLineBinding"] + items: [string, Expression, CommandLineBinding] jsonldPredicate: "_id": "cwl:arguments" "_container": "@list" - name: stdin - type: ["null", string, "#Expression"] + type: ["null", string, Expression] doc: | A path to a file whose contents must be piped into the command's standard input stream. - name: stderr - type: ["null", string, "#Expression"] + type: ["null", string, Expression] jsonldPredicate: "https://w3id.org/cwl/cwl#stderr" doc: | Capture the command's standard error stream to a file written to @@ -533,7 +533,7 @@ $graph: return value is not a string, or the resulting path contains illegal characters (such as the path separator `/`) it is an error. - name: stdout - type: ["null", string, "#Expression"] + type: ["null", string, Expression] jsonldPredicate: "https://w3id.org/cwl/cwl#stdout" doc: | Capture the command's standard output stream to a file written to @@ -546,28 +546,19 @@ $graph: return value is not a string, or the resulting path contains illegal characters (such as the path separator `/`) it is an error. - name: successCodes - type: - - "null" - - type: array - items: int + type: int[]? doc: | Exit codes that indicate the process completed successfully. - name: temporaryFailCodes - type: - - "null" - - type: array - items: int + type: int[]? doc: | Exit codes that indicate the process failed due to a possibly temporary condition, where excuting the process with the same runtime environment and inputs may produce different results. - name: permanentFailCodes - type: - - "null" - - type: array - items: int + type: int[]? doc: Exit codes that indicate the process failed due to a permanent logic error, where excuting the process with the same runtime environment and @@ -576,7 +567,7 @@ $graph: - type: record name: DockerRequirement - extends: "#ProcessRequirement" + extends: ProcessRequirement doc: | Indicates that a workflow component should be run in a [Docker](http://docker.com) container, and specifies how to fetch or build @@ -611,33 +602,33 @@ $graph: environment as defined by Docker. fields: - - name: "class" - type: "string" + - name: class + type: string doc: "Always 'DockerRequirement'" jsonldPredicate: "_id": "@type" "_type": "@vocab" - name: dockerPull - type: ["null", "string"] + type: string? doc: "Specify a Docker image to retrieve using `docker pull`." - - name: "dockerLoad" - type: ["null", "string"] + - name: dockerLoad + type: string? doc: "Specify a HTTP URL from which to download a Docker image using `docker load`." - name: dockerFile - type: ["null", "string"] + type: string? doc: "Supply the contents of a Dockerfile which will be built using `docker build`." - name: dockerImport - type: ["null", "string"] + type: string? doc: "Provide HTTP URL to download and gunzip a Docker images using `docker import." - name: dockerImageId - type: ["null", "string"] + type: string? doc: | 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. - name: dockerOutputDirectory - type: ["null", "string"] + type: string? doc: | Set the designated output directory to a specific location inside the Docker container. @@ -645,21 +636,19 @@ $graph: - type: record name: SoftwareRequirement - extends: "#ProcessRequirement" + extends: ProcessRequirement doc: | A list of software packages that should be configured in the environment of the defined process. fields: - - name: "class" - type: "string" + - name: class + type: string doc: "Always 'SoftwareRequirement'" jsonldPredicate: "_id": "@type" "_type": "@vocab" - name: packages - type: - type: array - items: SoftwarePackage + type: SoftwarePackage? doc: "The list of software to be configured." jsonldPredicate: mapSubject: name @@ -672,7 +661,7 @@ $graph: type: string doc: "The common name of the software to be configured." jsonldPredicate: "@id" - - name: "version" + - name: version type: string[]? doc: "The (optional) version of the software to configured." - name: specs @@ -744,9 +733,9 @@ $graph: workflow platform in the designated output directory prior to executing the command line tool. fields: - - name: "class" - type: "string" - doc: "InitialWorkDirRequirement" + - name: class + type: string + doc: InitialWorkDirRequirement jsonldPredicate: "_id": "@type" "_type": "@vocab" @@ -768,21 +757,19 @@ $graph: - name: EnvVarRequirement type: record - extends: "#ProcessRequirement" + extends: ProcessRequirement doc: | Define a list of environment variables which will be set in the execution environment of the tool. See `EnvironmentDef` for details. fields: - - name: "class" - type: "string" + - name: class + type: string doc: "Always 'EnvVarRequirement'" jsonldPredicate: "_id": "@type" "_type": "@vocab" - name: envDef - type: - type: "array" - items: "#EnvironmentDef" + type: EnvironmentDef[] doc: The list of environment variables. jsonldPredicate: mapSubject: envName @@ -791,7 +778,7 @@ $graph: - type: record name: ShellCommandRequirement - extends: "#ProcessRequirement" + extends: ProcessRequirement doc: | Modify the behavior of CommandLineTool to generate a single string containing a shell command line. Each item in the argument list must be @@ -801,8 +788,8 @@ $graph: argument is joined into the command string without quoting, which allows the use of shell metacharacters such as `|` for pipes. fields: - - name: "class" - type: "string" + - name: class + type: string doc: "Always 'ShellCommandRequirement'" jsonldPredicate: "_id": "@type" @@ -811,7 +798,7 @@ $graph: - type: record name: ResourceRequirement - extends: "#ProcessRequirement" + extends: ProcessRequirement doc: | Specify basic hardware resource requirements. @@ -835,40 +822,40 @@ $graph: If neither "min" nor "max" is specified for a resource, an implementation may provide a default. fields: - - name: "class" - type: "string" + - name: class + type: string doc: "Always 'ResourceRequirement'" jsonldPredicate: "_id": "@type" "_type": "@vocab" - name: coresMin - type: ["null", long, string, "#Expression"] + type: ["null", long, string, Expression] doc: Minimum reserved number of CPU cores - name: coresMax - type: ["null", int, string, "#Expression"] + type: ["null", int, string, Expression] doc: Maximum reserved number of CPU cores - name: ramMin - type: ["null", long, string, "#Expression"] + type: ["null", long, string, Expression] doc: Minimum reserved RAM in mebibytes (2**20) - name: ramMax - type: ["null", long, string, "#Expression"] + type: ["null", long, string, Expression] doc: Maximum reserved RAM in mebibytes (2**20) - name: tmpdirMin - type: ["null", long, string, "#Expression"] + type: ["null", long, string, Expression] doc: Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) - name: tmpdirMax - type: ["null", long, string, "#Expression"] + type: ["null", long, string, Expression] doc: Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) - name: outdirMin - type: ["null", long, string, "#Expression"] + type: ["null", long, string, Expression] doc: Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) - name: outdirMax - type: ["null", long, string, "#Expression"] + type: ["null", long, string, Expression] doc: Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) diff --git a/cwltool/schemas/v1.0/Process.yml b/cwltool/schemas/v1.0/Process.yml index df6923d47..1526d9d26 100644 --- a/cwltool/schemas/v1.0/Process.yml +++ b/cwltool/schemas/v1.0/Process.yml @@ -35,6 +35,7 @@ $graph: - cwl:draft-4.dev2 - cwl:draft-4.dev3 - cwl:v1.0.dev4 + - cwl:v1.0 - name: CWLType type: enum @@ -158,12 +159,12 @@ $graph: The implementation must set this field automatically based on the value of `basename` prior to evaluating parameter references or expressions. - name: checksum - type: ["null", string] + type: string? doc: | Optional hash code for validating file integrity. Currently must be in the form "sha1$ + hexadecimal string" using the SHA-1 algorithm. - name: size - type: ["null", long] + type: long? doc: Optional file size. - name: "secondaryFiles" type: @@ -179,7 +180,7 @@ $graph: `secondaryFiles` may itself include `secondaryFiles` for which the same rules apply. - name: format - type: ["null", string] + type: string? jsonldPredicate: _id: cwl:format _type: "@id" @@ -316,7 +317,7 @@ $graph: - name: Parameter type: record - extends: "#SchemaBase" + extends: SchemaBase abstract: true doc: | Define an input or output parameter to a process. @@ -325,10 +326,10 @@ $graph: - name: secondaryFiles type: - "null" - - "string" - - "#Expression" - - type: "array" - items: ["string", "#Expression"] + - string + - Expression + - type: array + items: [string, Expression] jsonldPredicate: "cwl:secondaryFiles" doc: | Only valid when `type: File` or is an array of `items: File`. @@ -353,7 +354,7 @@ $graph: - string - type: array items: string - - "#Expression" + - Expression jsonldPredicate: _id: cwl:format _type: "@id" @@ -370,7 +371,7 @@ $graph: the output parameter. - name: streamable - type: ["null", "boolean"] + type: boolean? doc: | Only valid when `type: File` or is an array of `items: File`. @@ -420,13 +421,13 @@ $graph: - name: InputSchema - extends: "#SchemaBase" + extends: SchemaBase type: record abstract: true - name: OutputSchema - extends: "#SchemaBase" + extends: SchemaBase type: record abstract: true @@ -436,16 +437,16 @@ $graph: extends: "sld:RecordField" specialize: - specializeFrom: "sld:RecordSchema" - specializeTo: "#InputRecordSchema" + specializeTo: InputRecordSchema - specializeFrom: "sld:EnumSchema" - specializeTo: "#InputEnumSchema" + specializeTo: InputEnumSchema - specializeFrom: "sld:ArraySchema" - specializeTo: "#InputArraySchema" + specializeTo: InputArraySchema - specializeFrom: "sld:PrimitiveType" - specializeTo: "#CWLType" + specializeTo: CWLType fields: - name: inputBinding - type: [ "null", "#InputBinding" ] + type: InputBinding? jsonldPredicate: "cwl:inputBinding" - name: label type: string? @@ -455,36 +456,36 @@ $graph: - name: InputRecordSchema type: record - extends: ["sld:RecordSchema", "#InputSchema"] + extends: ["sld:RecordSchema", InputSchema] specialize: - specializeFrom: "sld:RecordField" - specializeTo: "#InputRecordField" + specializeTo: InputRecordField - name: InputEnumSchema type: record - extends: ["sld:EnumSchema", "#InputSchema"] + extends: ["sld:EnumSchema", InputSchema] fields: - name: inputBinding - type: [ "null", "#InputBinding" ] + type: InputBinding? jsonldPredicate: "cwl:inputBinding" - name: InputArraySchema type: record - extends: ["sld:ArraySchema", "#InputSchema"] + extends: ["sld:ArraySchema", InputSchema] specialize: - specializeFrom: "sld:RecordSchema" - specializeTo: "#InputRecordSchema" + specializeTo: InputRecordSchema - specializeFrom: "sld:EnumSchema" - specializeTo: "#InputEnumSchema" + specializeTo: InputEnumSchema - specializeFrom: "sld:ArraySchema" - specializeTo: "#InputArraySchema" + specializeTo: InputArraySchema - specializeFrom: "sld:PrimitiveType" - specializeTo: "#CWLType" + specializeTo: CWLType fields: - name: inputBinding - type: [ "null", "#InputBinding" ] + type: InputBinding? jsonldPredicate: "cwl:inputBinding" @@ -493,16 +494,16 @@ $graph: extends: "sld:RecordField" specialize: - specializeFrom: "sld:RecordSchema" - specializeTo: "#OutputRecordSchema" + specializeTo: OutputRecordSchema - specializeFrom: "sld:EnumSchema" - specializeTo: "#OutputEnumSchema" + specializeTo: OutputEnumSchema - specializeFrom: "sld:ArraySchema" - specializeTo: "#OutputArraySchema" + specializeTo: OutputArraySchema - specializeFrom: "sld:PrimitiveType" - specializeTo: "#CWLType" + specializeTo: CWLType fields: - name: outputBinding - type: [ "null", "#OutputBinding" ] + type: OutputBinding? jsonldPredicate: "cwl:outputBinding" @@ -512,55 +513,55 @@ $graph: docParent: "#OutputParameter" specialize: - specializeFrom: "sld:RecordField" - specializeTo: "#OutputRecordField" + specializeTo: OutputRecordField - name: OutputEnumSchema type: record - extends: ["sld:EnumSchema", "#OutputSchema"] + extends: ["sld:EnumSchema", OutputSchema] docParent: "#OutputParameter" fields: - name: outputBinding - type: [ "null", "#OutputBinding" ] + type: OutputBinding? jsonldPredicate: "cwl:outputBinding" - name: OutputArraySchema type: record - extends: ["sld:ArraySchema", "#OutputSchema"] + extends: ["sld:ArraySchema", OutputSchema] docParent: "#OutputParameter" specialize: - specializeFrom: "sld:RecordSchema" - specializeTo: "#OutputRecordSchema" + specializeTo: OutputRecordSchema - specializeFrom: "sld:EnumSchema" - specializeTo: "#OutputEnumSchema" + specializeTo: OutputEnumSchema - specializeFrom: "sld:ArraySchema" - specializeTo: "#OutputArraySchema" + specializeTo: OutputArraySchema - specializeFrom: "sld:PrimitiveType" - specializeTo: "#CWLType" + specializeTo: CWLType fields: - name: outputBinding - type: [ "null", "#OutputBinding" ] + type: OutputBinding? jsonldPredicate: "cwl:outputBinding" - name: InputParameter type: record - extends: "#Parameter" + extends: Parameter fields: - name: id type: string jsonldPredicate: "@id" doc: "The unique identifier for this parameter object." - - name: "inputBinding" - type: [ "null", "#InputBinding" ] + - name: inputBinding + type: InputBinding? jsonldPredicate: "cwl:inputBinding" doc: | Describes how to handle the inputs of a process and convert them into a concrete form for execution, such as command line parameters. - name: default - type: ["null", "Any"] + type: Any? jsonldPredicate: "cwl:default" doc: | The default value for this parameter if not provided in the input @@ -569,17 +570,17 @@ $graph: - name: type type: - "null" - - "#CWLType" - - "#InputRecordSchema" - - "#InputEnumSchema" - - "#InputArraySchema" + - CWLType + - InputRecordSchema + - InputEnumSchema + - InputArraySchema - string - type: array items: - - "#CWLType" - - "#InputRecordSchema" - - "#InputEnumSchema" - - "#InputArraySchema" + - CWLType + - InputRecordSchema + - InputEnumSchema + - InputArraySchema - string jsonldPredicate: "_id": "sld:type" @@ -591,14 +592,14 @@ $graph: - name: OutputParameter type: record - extends: "#Parameter" + extends: Parameter fields: - name: id type: string jsonldPredicate: "@id" doc: "The unique identifier for this parameter object." - - name: "outputBinding" - type: [ "null", "#OutputBinding" ] + - name: outputBinding + type: OutputBinding? jsonldPredicate: "cwl:outputBinding" doc: | Describes how to handle the outputs of a process. @@ -627,13 +628,13 @@ $graph: fields: - name: id - type: ["null", string] + type: string? jsonldPredicate: "@id" doc: "The unique identifier for this process object." - name: inputs type: type: array - items: "#InputParameter" + items: InputParameter jsonldPredicate: _id: "cwl:inputs" mapSubject: id @@ -647,7 +648,7 @@ $graph: - name: outputs type: type: array - items: "#OutputParameter" + items: OutputParameter jsonldPredicate: _id: "cwl:outputs" mapSubject: id @@ -656,10 +657,7 @@ $graph: Defines the parameters representing the output of the process. May be used to generate and/or validate the output object. - name: requirements - type: - - "null" - - type: array - items: "#ProcessRequirement" + type: ProcessRequirement[]? jsonldPredicate: _id: "cwl:requirements" mapSubject: class @@ -671,10 +669,7 @@ $graph: error and the implementation must not attempt to run the process, unless overridden at user option. - name: hints - type: - - "null" - - type: array - items: Any + type: Any[]? doc: | Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this process. It is @@ -685,15 +680,11 @@ $graph: noLinkCheck: true mapSubject: class - name: label - type: - - "null" - - string + type: string? jsonldPredicate: "rdfs:label" doc: "A short, human-readable label of this process object." - name: doc - type: - - "null" - - string + type: string? jsonldPredicate: "rdfs:comment" doc: "A long, human-readable description of this process object." - name: cwlVersion @@ -707,23 +698,20 @@ $graph: - name: InlineJavascriptRequirement type: record - extends: "#ProcessRequirement" + extends: ProcessRequirement doc: | Indicates that the workflow platform must support inline Javascript expressions. If this requirement is not present, the workflow platform must not perform expression interpolatation. fields: - - name: "class" - type: "string" + - name: class + type: string doc: "Always 'InlineJavascriptRequirement'" jsonldPredicate: "_id": "@type" "_type": "@vocab" - name: expressionLib - type: - - "null" - - type: array - items: string + type: string[]? doc: | Additional code fragments that will also be inserted before executing the expression code. Allows for function definitions that may @@ -732,7 +720,7 @@ $graph: - name: SchemaDefRequirement type: record - extends: "#ProcessRequirement" + extends: ProcessRequirement doc: | This field consists of an array of type definitions which must be used when interpreting the `inputs` and `outputs` fields. When a `type` field @@ -742,8 +730,8 @@ $graph: processed in the order listed such that later schema definitions may refer to earlier schema definitions. fields: - - name: "class" - type: "string" + - name: class + type: string doc: "Always 'SchemaDefRequirement'" jsonldPredicate: "_id": "@type" @@ -751,5 +739,5 @@ $graph: - name: types type: type: array - items: "#InputSchema" + items: InputSchema doc: The list of type definitions. diff --git a/cwltool/schemas/v1.0/v1.0/binding-test.cwl b/cwltool/schemas/v1.0/v1.0/binding-test.cwl index e93b347d8..8415dc414 100755 --- a/cwltool/schemas/v1.0/v1.0/binding-test.cwl +++ b/cwltool/schemas/v1.0/v1.0/binding-test.cwl @@ -1,7 +1,7 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: - id: reference diff --git a/cwltool/schemas/v1.0/v1.0/bwa-mem-tool.cwl b/cwltool/schemas/v1.0/v1.0/bwa-mem-tool.cwl index d77376871..110189ffc 100755 --- a/cwltool/schemas/v1.0/v1.0/bwa-mem-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/bwa-mem-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 class: CommandLineTool diff --git a/cwltool/schemas/v1.0/v1.0/cat1-testcli.cwl b/cwltool/schemas/v1.0/v1.0/cat1-testcli.cwl index 657a27e89..06782c2b9 100755 --- a/cwltool/schemas/v1.0/v1.0/cat1-testcli.cwl +++ b/cwltool/schemas/v1.0/v1.0/cat1-testcli.cwl @@ -1,7 +1,7 @@ #!/usr/bin/env cwl-runner { "class": "CommandLineTool", - "cwlVersion": "v1.0.dev4", + "cwlVersion": "v1.0", "doc": "Print the contents of a file to stdout using 'cat' running in a docker container.", "inputs": [ { diff --git a/cwltool/schemas/v1.0/v1.0/cat1-tool.cwl b/cwltool/schemas/v1.0/v1.0/cat1-tool.cwl index 4df6cf2b6..c0f23ec81 100755 --- a/cwltool/schemas/v1.0/v1.0/cat1-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/cat1-tool.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 class: CommandLineTool doc: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: diff --git a/cwltool/schemas/v1.0/v1.0/cat2-tool.cwl b/cwltool/schemas/v1.0/v1.0/cat2-tool.cwl index 72799d81d..c34762d78 100755 --- a/cwltool/schemas/v1.0/v1.0/cat2-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/cat2-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 doc: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/v1.0/v1.0/cat3-tool-mediumcut.cwl b/cwltool/schemas/v1.0/v1.0/cat3-tool-mediumcut.cwl index 70ed04ede..81958c530 100755 --- a/cwltool/schemas/v1.0/v1.0/cat3-tool-mediumcut.cwl +++ b/cwltool/schemas/v1.0/v1.0/cat3-tool-mediumcut.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 doc: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/v1.0/v1.0/cat3-tool-shortcut.cwl b/cwltool/schemas/v1.0/v1.0/cat3-tool-shortcut.cwl index 166757345..0f1694bc2 100755 --- a/cwltool/schemas/v1.0/v1.0/cat3-tool-shortcut.cwl +++ b/cwltool/schemas/v1.0/v1.0/cat3-tool-shortcut.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 doc: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/v1.0/v1.0/cat3-tool.cwl b/cwltool/schemas/v1.0/v1.0/cat3-tool.cwl index f51c1bf3c..c019c88cc 100755 --- a/cwltool/schemas/v1.0/v1.0/cat3-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/cat3-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 doc: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/v1.0/v1.0/cat4-tool.cwl b/cwltool/schemas/v1.0/v1.0/cat4-tool.cwl index 9a0c72795..f3d8956c0 100755 --- a/cwltool/schemas/v1.0/v1.0/cat4-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/cat4-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 doc: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/v1.0/v1.0/cat5-tool.cwl b/cwltool/schemas/v1.0/v1.0/cat5-tool.cwl index 4769e5eba..e5ae681cc 100755 --- a/cwltool/schemas/v1.0/v1.0/cat5-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/cat5-tool.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 class: CommandLineTool doc: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: diff --git a/cwltool/schemas/v1.0/v1.0/conflict-wf.cwl b/cwltool/schemas/v1.0/v1.0/conflict-wf.cwl index f8cb8604d..2047e96cb 100644 --- a/cwltool/schemas/v1.0/v1.0/conflict-wf.cwl +++ b/cwltool/schemas/v1.0/v1.0/conflict-wf.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 $graph: - id: echo class: CommandLineTool diff --git a/cwltool/schemas/v1.0/v1.0/count-lines1-wf.cwl b/cwltool/schemas/v1.0/v1.0/count-lines1-wf.cwl index dd5b9adb6..77cbf3aa0 100755 --- a/cwltool/schemas/v1.0/v1.0/count-lines1-wf.cwl +++ b/cwltool/schemas/v1.0/v1.0/count-lines1-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: file1: diff --git a/cwltool/schemas/v1.0/v1.0/count-lines2-wf.cwl b/cwltool/schemas/v1.0/v1.0/count-lines2-wf.cwl index ce66ba3dd..be564beaf 100755 --- a/cwltool/schemas/v1.0/v1.0/count-lines2-wf.cwl +++ b/cwltool/schemas/v1.0/v1.0/count-lines2-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 requirements: InlineJavascriptRequirement: {} diff --git a/cwltool/schemas/v1.0/v1.0/count-lines3-wf.cwl b/cwltool/schemas/v1.0/v1.0/count-lines3-wf.cwl index b33d0fef8..0d89a9ff5 100755 --- a/cwltool/schemas/v1.0/v1.0/count-lines3-wf.cwl +++ b/cwltool/schemas/v1.0/v1.0/count-lines3-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: file1: diff --git a/cwltool/schemas/v1.0/v1.0/count-lines4-wf.cwl b/cwltool/schemas/v1.0/v1.0/count-lines4-wf.cwl index cf458bcc7..cad8367ac 100755 --- a/cwltool/schemas/v1.0/v1.0/count-lines4-wf.cwl +++ b/cwltool/schemas/v1.0/v1.0/count-lines4-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: file1: diff --git a/cwltool/schemas/v1.0/v1.0/count-lines5-wf.cwl b/cwltool/schemas/v1.0/v1.0/count-lines5-wf.cwl index 67e23d16c..cdc85a361 100755 --- a/cwltool/schemas/v1.0/v1.0/count-lines5-wf.cwl +++ b/cwltool/schemas/v1.0/v1.0/count-lines5-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: file1: diff --git a/cwltool/schemas/v1.0/v1.0/count-lines6-wf.cwl b/cwltool/schemas/v1.0/v1.0/count-lines6-wf.cwl index b22214e3b..50d71ef12 100755 --- a/cwltool/schemas/v1.0/v1.0/count-lines6-wf.cwl +++ b/cwltool/schemas/v1.0/v1.0/count-lines6-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: file1: File[] diff --git a/cwltool/schemas/v1.0/v1.0/count-lines7-wf.cwl b/cwltool/schemas/v1.0/v1.0/count-lines7-wf.cwl index 11e016a30..8cae70883 100755 --- a/cwltool/schemas/v1.0/v1.0/count-lines7-wf.cwl +++ b/cwltool/schemas/v1.0/v1.0/count-lines7-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 requirements: - class: MultipleInputFeatureRequirement diff --git a/cwltool/schemas/v1.0/v1.0/count-lines8-wf.cwl b/cwltool/schemas/v1.0/v1.0/count-lines8-wf.cwl index 2d80666b6..3211e3b17 100755 --- a/cwltool/schemas/v1.0/v1.0/count-lines8-wf.cwl +++ b/cwltool/schemas/v1.0/v1.0/count-lines8-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: file1: File diff --git a/cwltool/schemas/v1.0/v1.0/count-lines9-wf.cwl b/cwltool/schemas/v1.0/v1.0/count-lines9-wf.cwl index 0e6075ccf..ea751deb7 100755 --- a/cwltool/schemas/v1.0/v1.0/count-lines9-wf.cwl +++ b/cwltool/schemas/v1.0/v1.0/count-lines9-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: [] diff --git a/cwltool/schemas/v1.0/v1.0/dir.cwl b/cwltool/schemas/v1.0/v1.0/dir.cwl index 14ac1ef32..9c08006fd 100644 --- a/cwltool/schemas/v1.0/v1.0/dir.cwl +++ b/cwltool/schemas/v1.0/v1.0/dir.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 requirements: - class: ShellCommandRequirement inputs: diff --git a/cwltool/schemas/v1.0/v1.0/dir2.cwl b/cwltool/schemas/v1.0/v1.0/dir2.cwl index e3309d76b..01599d45b 100644 --- a/cwltool/schemas/v1.0/v1.0/dir2.cwl +++ b/cwltool/schemas/v1.0/v1.0/dir2.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 hints: DockerRequirement: dockerPull: debian:8 diff --git a/cwltool/schemas/v1.0/v1.0/dir3.cwl b/cwltool/schemas/v1.0/v1.0/dir3.cwl index ac306a219..36b56cfc7 100644 --- a/cwltool/schemas/v1.0/v1.0/dir3.cwl +++ b/cwltool/schemas/v1.0/v1.0/dir3.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 baseCommand: [tar, xvf] inputs: inf: diff --git a/cwltool/schemas/v1.0/v1.0/dir4.cwl b/cwltool/schemas/v1.0/v1.0/dir4.cwl index 6fd7583b2..b2019a2c2 100644 --- a/cwltool/schemas/v1.0/v1.0/dir4.cwl +++ b/cwltool/schemas/v1.0/v1.0/dir4.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 requirements: - class: ShellCommandRequirement inputs: diff --git a/cwltool/schemas/v1.0/v1.0/dir5.cwl b/cwltool/schemas/v1.0/v1.0/dir5.cwl index 5b26f4d40..8b2bb23bd 100644 --- a/cwltool/schemas/v1.0/v1.0/dir5.cwl +++ b/cwltool/schemas/v1.0/v1.0/dir5.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 requirements: - class: ShellCommandRequirement - class: InitialWorkDirRequirement diff --git a/cwltool/schemas/v1.0/v1.0/echo-tool.cwl b/cwltool/schemas/v1.0/v1.0/echo-tool.cwl index f46abb30f..023369326 100644 --- a/cwltool/schemas/v1.0/v1.0/echo-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/echo-tool.cwl @@ -1,7 +1,7 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: in: type: Any diff --git a/cwltool/schemas/v1.0/v1.0/egrep-stderr-mediumcut.cwl b/cwltool/schemas/v1.0/v1.0/egrep-stderr-mediumcut.cwl index 31285f10b..ca2732c6f 100644 --- a/cwltool/schemas/v1.0/v1.0/egrep-stderr-mediumcut.cwl +++ b/cwltool/schemas/v1.0/v1.0/egrep-stderr-mediumcut.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 doc: "Test of capturing stderr output in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/v1.0/v1.0/egrep-stderr-shortcut.cwl b/cwltool/schemas/v1.0/v1.0/egrep-stderr-shortcut.cwl index ae75f4a45..b9088da54 100644 --- a/cwltool/schemas/v1.0/v1.0/egrep-stderr-shortcut.cwl +++ b/cwltool/schemas/v1.0/v1.0/egrep-stderr-shortcut.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 doc: "Test of capturing stderr output in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/v1.0/v1.0/egrep-stderr.cwl b/cwltool/schemas/v1.0/v1.0/egrep-stderr.cwl index 896575325..d7a8814b9 100644 --- a/cwltool/schemas/v1.0/v1.0/egrep-stderr.cwl +++ b/cwltool/schemas/v1.0/v1.0/egrep-stderr.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 doc: "Test of capturing stderr output in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/v1.0/v1.0/env-tool1.cwl b/cwltool/schemas/v1.0/v1.0/env-tool1.cwl index 145dffc54..1d0e0966b 100644 --- a/cwltool/schemas/v1.0/v1.0/env-tool1.cwl +++ b/cwltool/schemas/v1.0/v1.0/env-tool1.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: in: string outputs: diff --git a/cwltool/schemas/v1.0/v1.0/env-tool2.cwl b/cwltool/schemas/v1.0/v1.0/env-tool2.cwl index e8726d0e2..bcd5b6279 100644 --- a/cwltool/schemas/v1.0/v1.0/env-tool2.cwl +++ b/cwltool/schemas/v1.0/v1.0/env-tool2.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: in: string outputs: diff --git a/cwltool/schemas/v1.0/v1.0/env-wf1.cwl b/cwltool/schemas/v1.0/v1.0/env-wf1.cwl index eb99ac230..f5cd51715 100644 --- a/cwltool/schemas/v1.0/v1.0/env-wf1.cwl +++ b/cwltool/schemas/v1.0/v1.0/env-wf1.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: in: string diff --git a/cwltool/schemas/v1.0/v1.0/env-wf2.cwl b/cwltool/schemas/v1.0/v1.0/env-wf2.cwl index 10d986a94..8a89b5796 100644 --- a/cwltool/schemas/v1.0/v1.0/env-wf2.cwl +++ b/cwltool/schemas/v1.0/v1.0/env-wf2.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: in: string diff --git a/cwltool/schemas/v1.0/v1.0/formattest.cwl b/cwltool/schemas/v1.0/v1.0/formattest.cwl index c1b82ee5b..19168e875 100644 --- a/cwltool/schemas/v1.0/v1.0/formattest.cwl +++ b/cwltool/schemas/v1.0/v1.0/formattest.cwl @@ -1,6 +1,6 @@ $namespaces: edam: "http://edamontology.org/" -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 class: CommandLineTool doc: "Reverse each line using the `rev` command" inputs: diff --git a/cwltool/schemas/v1.0/v1.0/formattest2.cwl b/cwltool/schemas/v1.0/v1.0/formattest2.cwl index f4e0b6051..54acd4a24 100644 --- a/cwltool/schemas/v1.0/v1.0/formattest2.cwl +++ b/cwltool/schemas/v1.0/v1.0/formattest2.cwl @@ -3,7 +3,7 @@ $namespaces: $schemas: - EDAM.owl class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 doc: "Reverse each line using the `rev` command" inputs: diff --git a/cwltool/schemas/v1.0/v1.0/formattest3.cwl b/cwltool/schemas/v1.0/v1.0/formattest3.cwl index 1df27dd61..d0baf604a 100644 --- a/cwltool/schemas/v1.0/v1.0/formattest3.cwl +++ b/cwltool/schemas/v1.0/v1.0/formattest3.cwl @@ -5,7 +5,7 @@ $schemas: - EDAM.owl - gx_edam.ttl class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 doc: "Reverse each line using the `rev` command" inputs: diff --git a/cwltool/schemas/v1.0/v1.0/glob-expr-list.cwl b/cwltool/schemas/v1.0/v1.0/glob-expr-list.cwl index b2784b614..a70bccf4a 100644 --- a/cwltool/schemas/v1.0/v1.0/glob-expr-list.cwl +++ b/cwltool/schemas/v1.0/v1.0/glob-expr-list.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: ids: diff --git a/cwltool/schemas/v1.0/v1.0/metadata.cwl b/cwltool/schemas/v1.0/v1.0/metadata.cwl index 91bba9833..c80e5b6c0 100644 --- a/cwltool/schemas/v1.0/v1.0/metadata.cwl +++ b/cwltool/schemas/v1.0/v1.0/metadata.cwl @@ -6,7 +6,7 @@ $schemas: - foaf.rdf - dcterms.rdf -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 class: CommandLineTool doc: "Print the contents of a file to stdout using 'cat' running in a docker container." diff --git a/cwltool/schemas/v1.0/v1.0/null-expression1-tool.cwl b/cwltool/schemas/v1.0/v1.0/null-expression1-tool.cwl index 7f34f3412..828fcfe89 100644 --- a/cwltool/schemas/v1.0/v1.0/null-expression1-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/null-expression1-tool.cwl @@ -3,7 +3,7 @@ class: ExpressionTool requirements: - class: InlineJavascriptRequirement -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: i1: diff --git a/cwltool/schemas/v1.0/v1.0/null-expression2-tool.cwl b/cwltool/schemas/v1.0/v1.0/null-expression2-tool.cwl index 50259b4b8..9c9e8c1a6 100644 --- a/cwltool/schemas/v1.0/v1.0/null-expression2-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/null-expression2-tool.cwl @@ -3,7 +3,7 @@ class: ExpressionTool requirements: - class: InlineJavascriptRequirement -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: i1: Any diff --git a/cwltool/schemas/v1.0/v1.0/optional-output.cwl b/cwltool/schemas/v1.0/v1.0/optional-output.cwl index 082f480f6..4172436b1 100644 --- a/cwltool/schemas/v1.0/v1.0/optional-output.cwl +++ b/cwltool/schemas/v1.0/v1.0/optional-output.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: "v1.0.dev4" +cwlVersion: "v1.0" doc: "Print the contents of a file to stdout using 'cat' running in a docker container." hints: DockerRequirement: diff --git a/cwltool/schemas/v1.0/v1.0/params.cwl b/cwltool/schemas/v1.0/v1.0/params.cwl index 0c113ac38..7b52f83b9 100644 --- a/cwltool/schemas/v1.0/v1.0/params.cwl +++ b/cwltool/schemas/v1.0/v1.0/params.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: bar: type: Any diff --git a/cwltool/schemas/v1.0/v1.0/params2.cwl b/cwltool/schemas/v1.0/v1.0/params2.cwl index 78cbf88af..6d8061620 100644 --- a/cwltool/schemas/v1.0/v1.0/params2.cwl +++ b/cwltool/schemas/v1.0/v1.0/params2.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 requirements: - class: InlineJavascriptRequirement diff --git a/cwltool/schemas/v1.0/v1.0/parseInt-tool.cwl b/cwltool/schemas/v1.0/v1.0/parseInt-tool.cwl index 09a160f4d..42f166bde 100755 --- a/cwltool/schemas/v1.0/v1.0/parseInt-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/parseInt-tool.cwl @@ -3,7 +3,7 @@ class: ExpressionTool requirements: - class: InlineJavascriptRequirement -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: file1: diff --git a/cwltool/schemas/v1.0/v1.0/record-output.cwl b/cwltool/schemas/v1.0/v1.0/record-output.cwl index c397912e3..bf90d3e16 100644 --- a/cwltool/schemas/v1.0/v1.0/record-output.cwl +++ b/cwltool/schemas/v1.0/v1.0/record-output.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 requirements: - class: ShellCommandRequirement inputs: diff --git a/cwltool/schemas/v1.0/v1.0/rename.cwl b/cwltool/schemas/v1.0/v1.0/rename.cwl index 37d29a297..2326e7fad 100644 --- a/cwltool/schemas/v1.0/v1.0/rename.cwl +++ b/cwltool/schemas/v1.0/v1.0/rename.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 baseCommand: "true" requirements: InitialWorkDirRequirement: diff --git a/cwltool/schemas/v1.0/v1.0/revsort.cwl b/cwltool/schemas/v1.0/v1.0/revsort.cwl index 13a533e34..a6b2774ad 100644 --- a/cwltool/schemas/v1.0/v1.0/revsort.cwl +++ b/cwltool/schemas/v1.0/v1.0/revsort.cwl @@ -3,7 +3,7 @@ # class: Workflow doc: "Reverse the lines in a document, then sort those lines." -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 # Requirements & hints specify prerequisites and extensions to the workflow. # In this example, DockerRequirement specifies a default Docker container diff --git a/cwltool/schemas/v1.0/v1.0/revtool.cwl b/cwltool/schemas/v1.0/v1.0/revtool.cwl index 1bf2aa320..7f279643a 100644 --- a/cwltool/schemas/v1.0/v1.0/revtool.cwl +++ b/cwltool/schemas/v1.0/v1.0/revtool.cwl @@ -2,7 +2,7 @@ # Simplest example command line program wrapper for the Unix tool "rev". # class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 doc: "Reverse each line using the `rev` command" # The "inputs" array defines the structure of the input object that describes diff --git a/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf1.cwl b/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf1.cwl index d74449718..f38d1ed15 100644 --- a/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf1.cwl +++ b/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf1.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 class: Workflow inputs: inp: diff --git a/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf2.cwl b/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf2.cwl index 6b632e8c5..aa12c4cf7 100644 --- a/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf2.cwl +++ b/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf2.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 class: Workflow inputs: diff --git a/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf3.cwl b/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf3.cwl index c1ef5245e..5d0e0d688 100644 --- a/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf3.cwl +++ b/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf3.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 $graph: - id: echo diff --git a/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf4.cwl b/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf4.cwl index 4a5aecc1b..1c8c078d6 100644 --- a/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf4.cwl +++ b/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf4.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 $graph: - id: echo class: CommandLineTool diff --git a/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf5.cwl b/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf5.cwl index db9719839..016eebfd4 100644 --- a/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf5.cwl +++ b/cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf5.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 class: Workflow inputs: inp: diff --git a/cwltool/schemas/v1.0/v1.0/scatter-wf1.cwl b/cwltool/schemas/v1.0/v1.0/scatter-wf1.cwl index 647e4f2dc..d47065860 100644 --- a/cwltool/schemas/v1.0/v1.0/scatter-wf1.cwl +++ b/cwltool/schemas/v1.0/v1.0/scatter-wf1.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 class: Workflow inputs: inp: string[] diff --git a/cwltool/schemas/v1.0/v1.0/scatter-wf2.cwl b/cwltool/schemas/v1.0/v1.0/scatter-wf2.cwl index 9a761cd58..e46b829c1 100644 --- a/cwltool/schemas/v1.0/v1.0/scatter-wf2.cwl +++ b/cwltool/schemas/v1.0/v1.0/scatter-wf2.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 class: Workflow inputs: diff --git a/cwltool/schemas/v1.0/v1.0/scatter-wf3.cwl b/cwltool/schemas/v1.0/v1.0/scatter-wf3.cwl index 0bc79a267..358a99fa8 100644 --- a/cwltool/schemas/v1.0/v1.0/scatter-wf3.cwl +++ b/cwltool/schemas/v1.0/v1.0/scatter-wf3.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 $graph: - id: echo diff --git a/cwltool/schemas/v1.0/v1.0/scatter-wf4.cwl b/cwltool/schemas/v1.0/v1.0/scatter-wf4.cwl index 9138ddd11..e51db2f7a 100644 --- a/cwltool/schemas/v1.0/v1.0/scatter-wf4.cwl +++ b/cwltool/schemas/v1.0/v1.0/scatter-wf4.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 $graph: - id: echo class: CommandLineTool diff --git a/cwltool/schemas/v1.0/v1.0/schemadef-tool.cwl b/cwltool/schemas/v1.0/v1.0/schemadef-tool.cwl index b93549cdb..8b6ae9b3d 100644 --- a/cwltool/schemas/v1.0/v1.0/schemadef-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/schemadef-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 requirements: - $import: schemadef-type.yml - class: InlineJavascriptRequirement diff --git a/cwltool/schemas/v1.0/v1.0/schemadef-wf.cwl b/cwltool/schemas/v1.0/v1.0/schemadef-wf.cwl index 6a016679c..d3e38ebd8 100644 --- a/cwltool/schemas/v1.0/v1.0/schemadef-wf.cwl +++ b/cwltool/schemas/v1.0/v1.0/schemadef-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 class: Workflow requirements: diff --git a/cwltool/schemas/v1.0/v1.0/search.cwl b/cwltool/schemas/v1.0/v1.0/search.cwl index 952b04b93..9df391072 100644 --- a/cwltool/schemas/v1.0/v1.0/search.cwl +++ b/cwltool/schemas/v1.0/v1.0/search.cwl @@ -1,4 +1,4 @@ -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 $graph: - id: index class: CommandLineTool diff --git a/cwltool/schemas/v1.0/v1.0/shelltest.cwl b/cwltool/schemas/v1.0/v1.0/shelltest.cwl index c995ed5b2..3388b8b8b 100644 --- a/cwltool/schemas/v1.0/v1.0/shelltest.cwl +++ b/cwltool/schemas/v1.0/v1.0/shelltest.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 doc: "Reverse each line using the `rev` command then sort." requirements: - class: ShellCommandRequirement diff --git a/cwltool/schemas/v1.0/v1.0/sorttool.cwl b/cwltool/schemas/v1.0/v1.0/sorttool.cwl index 9e403477d..a4853217b 100644 --- a/cwltool/schemas/v1.0/v1.0/sorttool.cwl +++ b/cwltool/schemas/v1.0/v1.0/sorttool.cwl @@ -2,7 +2,7 @@ # demonstrating command line flags. class: CommandLineTool doc: "Sort lines using the `sort` command" -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 # This example is similar to the previous one, with an additional input # parameter called "reverse". It is a boolean parameter, which is diff --git a/cwltool/schemas/v1.0/v1.0/stagefile.cwl b/cwltool/schemas/v1.0/v1.0/stagefile.cwl index e09f59b63..b4a9b06a7 100644 --- a/cwltool/schemas/v1.0/v1.0/stagefile.cwl +++ b/cwltool/schemas/v1.0/v1.0/stagefile.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 requirements: InitialWorkDirRequirement: listing: diff --git a/cwltool/schemas/v1.0/v1.0/step-valuefrom-wf.cwl b/cwltool/schemas/v1.0/v1.0/step-valuefrom-wf.cwl index a73b37ac4..1b6d65e69 100644 --- a/cwltool/schemas/v1.0/v1.0/step-valuefrom-wf.cwl +++ b/cwltool/schemas/v1.0/v1.0/step-valuefrom-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 requirements: - class: StepInputExpressionRequirement diff --git a/cwltool/schemas/v1.0/v1.0/step-valuefrom2-wf.cwl b/cwltool/schemas/v1.0/v1.0/step-valuefrom2-wf.cwl index c13a9f662..2edb3f65f 100644 --- a/cwltool/schemas/v1.0/v1.0/step-valuefrom2-wf.cwl +++ b/cwltool/schemas/v1.0/v1.0/step-valuefrom2-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 requirements: - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement diff --git a/cwltool/schemas/v1.0/v1.0/step-valuefrom3-wf.cwl b/cwltool/schemas/v1.0/v1.0/step-valuefrom3-wf.cwl index ecdfdf9a3..f1974ddfe 100644 --- a/cwltool/schemas/v1.0/v1.0/step-valuefrom3-wf.cwl +++ b/cwltool/schemas/v1.0/v1.0/step-valuefrom3-wf.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: Workflow -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 requirements: - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement diff --git a/cwltool/schemas/v1.0/v1.0/template-tool.cwl b/cwltool/schemas/v1.0/v1.0/template-tool.cwl index 53393cb11..4722ccd56 100755 --- a/cwltool/schemas/v1.0/v1.0/template-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/template-tool.cwl @@ -1,5 +1,5 @@ #!/usr/bin/env cwl-runner -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 class: CommandLineTool requirements: - class: DockerRequirement diff --git a/cwltool/schemas/v1.0/v1.0/test-cwl-out.cwl b/cwltool/schemas/v1.0/v1.0/test-cwl-out.cwl index e18462b30..c40b096ff 100644 --- a/cwltool/schemas/v1.0/v1.0/test-cwl-out.cwl +++ b/cwltool/schemas/v1.0/v1.0/test-cwl-out.cwl @@ -1,5 +1,5 @@ class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 requirements: - class: ShellCommandRequirement - class: DockerRequirement diff --git a/cwltool/schemas/v1.0/v1.0/tmap-tool.cwl b/cwltool/schemas/v1.0/v1.0/tmap-tool.cwl index ef9748424..1cb08428b 100755 --- a/cwltool/schemas/v1.0/v1.0/tmap-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/tmap-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner { - "cwlVersion": "v1.0.dev4", + "cwlVersion": "v1.0", "class": "CommandLineTool", diff --git a/cwltool/schemas/v1.0/v1.0/wc-tool.cwl b/cwltool/schemas/v1.0/v1.0/wc-tool.cwl index 592b3cc50..d6265afb0 100755 --- a/cwltool/schemas/v1.0/v1.0/wc-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/wc-tool.cwl @@ -1,7 +1,7 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 inputs: file1: File diff --git a/cwltool/schemas/v1.0/v1.0/wc2-tool.cwl b/cwltool/schemas/v1.0/v1.0/wc2-tool.cwl index d0ff6419d..f1ad4587a 100755 --- a/cwltool/schemas/v1.0/v1.0/wc2-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/wc2-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 requirements: - class: InlineJavascriptRequirement diff --git a/cwltool/schemas/v1.0/v1.0/wc3-tool.cwl b/cwltool/schemas/v1.0/v1.0/wc3-tool.cwl index f9c7d03d2..2392eb7d9 100644 --- a/cwltool/schemas/v1.0/v1.0/wc3-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/wc3-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 requirements: - class: InlineJavascriptRequirement diff --git a/cwltool/schemas/v1.0/v1.0/wc4-tool.cwl b/cwltool/schemas/v1.0/v1.0/wc4-tool.cwl index 380fab372..f85e93444 100644 --- a/cwltool/schemas/v1.0/v1.0/wc4-tool.cwl +++ b/cwltool/schemas/v1.0/v1.0/wc4-tool.cwl @@ -1,6 +1,6 @@ #!/usr/bin/env cwl-runner class: CommandLineTool -cwlVersion: v1.0.dev4 +cwlVersion: v1.0 requirements: - class: InlineJavascriptRequirement diff --git a/cwltool/update.py b/cwltool/update.py index 16ca8d2da..3a0182ed7 100644 --- a/cwltool/update.py +++ b/cwltool/update.py @@ -426,9 +426,15 @@ def draft4Dev3to1_0dev4(doc, loader, baseuri): """Public updater for draft-4.dev3 to v1.0.dev4.""" return (_draft4Dev3to1_0dev4(doc, loader, baseuri), "v1.0.dev4") +def v1_0dev4to1_0(doc, loader, baseuri): + # type: (Any, Loader, str) -> Tuple[Any, str] + """Public updater for v1.0.dev4 to v1.0.""" + return (doc, "v1.0") + UPDATES = { "draft-2": draft2toDraft3dev1, - "draft-3": draft3toDraft4dev1 + "draft-3": draft3toDraft4dev1, + "v1.0": None } # type: Dict[unicode, Callable[[Any, Loader, str], Tuple[Any, str]]] DEVUPDATES = { @@ -440,13 +446,14 @@ def draft4Dev3to1_0dev4(doc, loader, baseuri): "draft-4.dev1": draft4Dev1toDev2, "draft-4.dev2": draft4Dev2toDev3, "draft-4.dev3": draft4Dev3to1_0dev4, - "v1.0.dev4": None + "v1.0.dev4": v1_0dev4to1_0, + "v1.0": None } # type: Dict[unicode, Callable[[Any, Loader, str], Tuple[Any, str]]] ALLUPDATES = UPDATES.copy() ALLUPDATES.update(DEVUPDATES) -LATEST = "v1.0.dev4" +LATEST = "v1.0" def identity(doc, loader, baseuri): # pylint: disable=unused-argument # type: (Any, Loader, str) -> Tuple[Any, Union[str, unicode]]