[System]
You are a helpful assistant that answers strictly in JSON. Here's the JSON schema you must adhere to:
<schema>
{"$ref":"#/definitions/CWLGraphOrFile","$schema":"http://json-schema.org/draft-07/schema#","definitions":{"CommandInputArraySchema":{"additionalProperties":false,"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputArraySchema","properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"inputBinding":{"$ref":"#/definitions/CommandLineBinding","description":"Describes how to turn this object into command line arguments."},"items":{"anyOf":[{"$ref":"#/definitions/CommandInputArraySchema"},{"$ref":"#/definitions/CommandInputRecordSchema"},{"$ref":"#/definitions/CommandInputEnumSchema"},{"items":{"anyOf":[{"$ref":"#/definitions/CommandInputArraySchema"},{"$ref":"#/definitions/CommandInputRecordSchema"},{"$ref":"#/definitions/CommandInputEnumSchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Defines the type of the array elements."},"label":{"description":"A short, human-readable label of this object.","type":"string"},"name":{"description":"The identifier for this type","type":"string"},"type":{"const":"array","description":"Must be `array`","type":"string"}},"required":["items","type"],"type":"object"},"CommandInputEnumSchema":{"additionalProperties":false,"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputEnumSchema","properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"inputBinding":{"$ref":"#/definitions/CommandLineBinding","description":"Describes how to turn this object into command line arguments."},"label":{"description":"A short, human-readable label of this object.","type":"string"},"name":{"description":"The identifier for this type","type":"string"},"symbols":{"description":"Defines the set of valid symbols.","items":{"type":"string"},"type":"array"},"type":{"const":"enum","description":"Must be `enum`","type":"string"}},"required":["symbols","type"],"type":"object"},"CommandInputParameter":{"additionalProperties":false,"description":"An input parameter for a CommandLineTool.","properties":{"default":{"description":"The default value to use for this parameter if the parameter is missing\nfrom the input object, or if the value of the parameter in the input\nobject is `null`.  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It may also be used to build a user\ninterface for constructing the input object.\n\nWhen accepting an input object, all input parameters must have a value.\nIf an input parameter is missing from the input object, it must be\nassigned a value of `null` (or the value of `default` for that\nparameter, if provided) for the purposes of validation and evaluation\nof expressions.","oneOf":[{"items":{"$ref":"#/definitions/CommandInputParameter"},"type":"array"},{"patternProperties":{"^[_a-zA-Z][a-zA-Z0-9_-]*$":{"oneOf":[{"$ref":"#/definitions/CommandInputParameter"},{"anyOf":[{"$ref":"#/definitions/CommandInputArraySchema"},{"$ref":"#/definitions/CommandInputRecordSchema"},{"$ref":"#/definitions/CommandInputEnumSchema"},{"items":{"anyOf":[{"$ref":"#/definitions/CommandInputArraySchema"},{"$ref":"#/definitions/CommandInputRecordSchema"},{"$ref":"#/definitions/CommandInputEnumSchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Specify valid types of data that may be assigned to this parameter."},{"type":"array","items":{"oneOf":[{"type":"string"},{"$ref":"#/definitions/CommandInputParameter"}]}}]}},"type":"object"}]},"intent":{"description":"An identifier for the type of computational operation, of this Process.\nEspecially useful for [`Operation`](Workflow.html#Operation), but can also be used for\n[`CommandLineTool`](CommandLineTool.html#CommandLineTool),\n[`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool).\n\nIf provided, then this must be an IRI of a concept node that\nrepresents the type of operation, preferably defined within an ontology.\n\nFor example, in the domain of bioinformatics, one can use an IRI from\nthe EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004),\nlike [Alignment](http://edamontology.org/operation_2928),\nor [Clustering](http://edamontology.org/operation_3432); or a more\nspecific Operation concept like\n[Split read mapping](http://edamontology.org/operation_3199).","items":{"type":"string"},"type":"array"},"label":{"description":"A short, human-readable label of this object.","type":"string"},"outputs":{"description":"Defines the parameters representing the output of the process.  May be\nused to generate and/or validate the output object.","oneOf":[{"items":{"$ref":"#/definitions/CommandOutputParameter"},"type":"array"},{"patternProperties":{"^[_a-zA-Z][a-zA-Z0-9_-]*$":{"oneOf":[{"$ref":"#/definitions/CommandOutputParameter"},{"anyOf":[{"$ref":"#/definitions/CommandOutputArraySchema"},{"$ref":"#/definitions/CommandOutputRecordSchema"},{"$ref":"#/definitions/CommandOutputEnumSchema"},{"items":{"anyOf":[{"$ref":"#/definitions/CommandOutputArraySchema"},{"$ref":"#/definitions/CommandOutputRecordSchema"},{"$ref":"#/definitions/CommandOutputEnumSchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Specify valid types of data that may be assigned to this parameter."},{"type":"array","items":{"oneOf":[{"type":"string"},{"$ref":"#/definitions/CommandOutputParameter"}]}}]}},"type":"object"}]},"permanentFailCodes":{"description":"Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail.\nIf not specified, all exit codes except 0 are considered permanent failure.","items":{"type":"number"},"type":"array"},"requirements":{"description":"Declares requirements that apply to either the runtime environment or the\nworkflow engine that must be met in order to execute this process.  If\nan implementation cannot satisfy all requirements, or a requirement is\nlisted which is not recognized by the implementation, it is a fatal\nerror and the implementation must not attempt to run the process,\nunless overridden at user option.","oneOf":[{"items":{"anyOf":[{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"},{"$ref":"#/definitions/InlineJavascriptRequirement"},{"$ref":"#/definitions/SchemaDefRequirement"},{"$ref":"#/definitions/LoadListingRequirement"},{"$ref":"#/definitions/DockerRequirement"},{"$ref":"#/definitions/SoftwareRequirement"},{"$ref":"#/definitions/InitialWorkDirRequirement"},{"$ref":"#/definitions/EnvVarRequirement"},{"$ref":"#/definitions/ShellCommandRequirement"},{"$ref":"#/definitions/ResourceRequirement"},{"$ref":"#/definitions/WorkReuse"},{"$ref":"#/definitions/NetworkAccess"},{"$ref":"#/definitions/InplaceUpdateRequirement"},{"$ref":"#/definitions/ToolTimeLimit"},{"$ref":"#/definitions/SubworkflowFeatureRequirement"},{"$ref":"#/definitions/ScatterFeatureRequirement"},{"$ref":"#/definitions/MultipleInputFeatureRequirement"},{"$ref":"#/definitions/StepInputExpressionRequirement"}]},"type":"array"},{"type":"object","properties":{"InlineJavascriptRequirement":{"anyOf":[{"$ref":"#/definitions/InlineJavascriptRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SchemaDefRequirement":{"anyOf":[{"$ref":"#/definitions/SchemaDefRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"LoadListingRequirement":{"anyOf":[{"$ref":"#/definitions/LoadListingRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"DockerRequirement":{"anyOf":[{"$ref":"#/definitions/DockerRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SoftwareRequirement":{"anyOf":[{"$ref":"#/definitions/SoftwareRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"InitialWorkDirRequirement":{"anyOf":[{"$ref":"#/definitions/InitialWorkDirRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"EnvVarRequirement":{"anyOf":[{"$ref":"#/definitions/EnvVarRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ShellCommandRequirement":{"anyOf":[{"$ref":"#/definitions/ShellCommandRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ResourceRequirement":{"anyOf":[{"$ref":"#/definitions/ResourceRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"WorkReuse":{"anyOf":[{"$ref":"#/definitions/WorkReuseMap"},{"type":"object","properties":{},"additionalProperties":false}]},"NetworkAccess":{"anyOf":[{"$ref":"#/definitions/NetworkAccessMap"},{"type":"object","properties":{},"additionalProperties":false}]},"InplaceUpdateRequirement":{"anyOf":[{"$ref":"#/definitions/InplaceUpdateRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ToolTimeLimit":{"anyOf":[{"$ref":"#/definitions/ToolTimeLimitMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SubworkflowFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/SubworkflowFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ScatterFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/ScatterFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"MultipleInputFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/MultipleInputFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"StepInputExpressionRequirement":{"anyOf":[{"$ref":"#/definitions/StepInputExpressionRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]}},"additionalProperties":false}]},"stderr":{"description":"Capture the command's standard error stream to a file written to\nthe designated output directory.\n\nIf `stderr` is a string, it specifies the file name to use.\n\nIf `stderr` is an expression, the expression is evaluated and must\nreturn a string with the file name to use to capture stderr.  If the\nreturn value is not a string, or the resulting path contains illegal\ncharacters (such as the path separator `/`) it is an error.","type":"string"},"stdin":{"description":"A path to a file whose contents must be piped into the command's\nstandard input stream.","type":"string"},"stdout":{"description":"Capture the command's standard output stream to a file written to\nthe designated output directory.\n\nIf the `CommandLineTool` contains logically chained commands\n(e.g. `echo a && echo b`) `stdout` must include the output of\nevery command.\n\nIf `stdout` is a string, it specifies the file name to use.\n\nIf `stdout` is an expression, the expression is evaluated and must\nreturn a string with the file name to use to capture stdout.  If the\nreturn value is not a string, or the resulting path contains illegal\ncharacters (such as the path separator `/`) it is an error.","type":"string"},"successCodes":{"description":"Exit codes that indicate the process completed successfully.\n\nIf not specified, only exit code 0 is considered success.","items":{"type":"number"},"type":"array"},"temporaryFailCodes":{"description":"Exit codes that indicate the process failed due to a possibly\ntemporary condition, where executing the process with the same\nruntime environment and inputs may produce different results.\n\nIf not specified, no exit codes are considered temporary failure.","items":{"type":"number"},"type":"array"}},"required":["class","inputs","outputs"],"type":"object"},"CommandOutputArraySchema":{"additionalProperties":false,"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputArraySchema","properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"items":{"anyOf":[{"$ref":"#/definitions/CommandOutputArraySchema"},{"$ref":"#/definitions/CommandOutputRecordSchema"},{"$ref":"#/definitions/CommandOutputEnumSchema"},{"items":{"anyOf":[{"$ref":"#/definitions/CommandOutputArraySchema"},{"$ref":"#/definitions/CommandOutputRecordSchema"},{"$ref":"#/definitions/CommandOutputEnumSchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Defines the type of the array elements."},"label":{"description":"A short, human-readable label of this object.","type":"string"},"name":{"description":"The identifier for this type","type":"string"},"type":{"const":"array","description":"Must be `array`","type":"string"}},"required":["items","type"],"type":"object"},"CommandOutputBinding":{"additionalProperties":false,"description":"Describes how to generate an output parameter based on the files produced\nby a CommandLineTool.\n\nThe output parameter value is generated by applying these operations in the\nfollowing order:\n\n  - glob\n  - loadContents\n  - outputEval\n  - secondaryFiles","properties":{"glob":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"Find files or directories relative to the output directory, using POSIX\nglob(3) pathname matching.  If an array is provided, find files or\ndirectories that match any pattern in the array.  If an expression is\nprovided, the expression must return a string or an array of strings,\nwhich will then be evaluated as one or more glob patterns.  Must only\nmatch and return files/directories which actually exist.\n\nIf the value of glob is a relative path pattern (does not\nbegin with a slash '/') then it is resolved relative to the\noutput directory.  If the value of the glob is an absolute\npath pattern (it does begin with a slash '/') then it must\nrefer to a path within the output directory.  It is an error\nif any glob resolves to a path outside the output directory.\nSpecifically this means globs that resolve to paths outside the output\ndirectory are illegal.\n\nA glob may match a path within the output directory which is\nactually a symlink to another file.  In this case, the\nexpected behavior is for the resulting File/Directory object to take the\n`basename` (and corresponding `nameroot` and `nameext`) of the\nsymlink.  The `location` of the File/Directory is implementation\ndependent, but logically the File/Directory should have the same content\nas the symlink target.  Platforms may stage output files/directories to\ncloud storage that lack the concept of a symlink.  In\nthis case file content and directories may be duplicated, or (to avoid\nduplication) the File/Directory `location` may refer to the symlink\ntarget.\n\nIt is an error if a symlink in the output directory (or any\nsymlink in a chain of links) refers to any file or directory\nthat is not under an input or output directory.\n\nImplementations may shut down a container before globbing\noutput, so globs and expressions must not assume access to the\ncontainer filesystem except for declared input and output."},"loadContents":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nIf true, the file (or each file in the array) must be a UTF-8\ntext file 64 KiB or smaller, and the implementation must read\nthe entire contents of the file (or file array) and place it\nin the `contents` field of the File object for use by\nexpressions.  If the size of the file is greater than 64 KiB,\nthe implementation must raise a fatal error.","type":"boolean"},"loadListing":{"description":"Only valid when `type: Directory` or is an array of `items: Directory`.\n\nSpecify the desired behavior for loading the `listing` field of\na Directory object for use by expressions.\n\nThe order of precedence for loadListing is:\n\n  1. `loadListing` on an individual parameter\n  2. Inherited from `LoadListingRequirement`\n  3. By default: `no_listing`","enum":["deep_listing","no_listing","shallow_listing"],"type":"string"},"outputEval":{"description":"Evaluate an expression to generate the output value.  If\n`glob` was specified, the value of `self` must be an array\ncontaining file objects that were matched.  If no files were\nmatched, `self` must be a zero length array; if a single file\nwas matched, the value of `self` is an array of a single\nelement.  The exit code of the process is\navailable in the expression as `runtime.exitCode`.\n\nAdditionally, if `loadContents` is true, the file must be a\nUTF-8 text file 64 KiB or smaller, and the implementation must\nread the entire contents of the file (or file array) and place\nit in the `contents` field of the File object for use in\n`outputEval`.  If the size of the file is greater than 64 KiB,\nthe implementation must raise a fatal error.\n\nIf a tool needs to return a large amount of structured data to\nthe workflow, loading the output object from `cwl.output.json`\nbypasses `outputEval` and is not subject to the 64 KiB\n`loadContents` limit.","type":"string"}},"required":[],"type":"object"},"CommandOutputEnumSchema":{"additionalProperties":false,"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputEnumSchema","properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"label":{"description":"A short, human-readable label of this object.","type":"string"},"name":{"description":"The identifier for this type","type":"string"},"symbols":{"description":"Defines the set of valid symbols.","items":{"type":"string"},"type":"array"},"type":{"const":"enum","description":"Must be `enum`","type":"string"}},"required":["symbols","type"],"type":"object"},"CommandOutputParameter":{"additionalProperties":false,"description":"An output parameter for a CommandLineTool.","properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"format":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nThis is the file format that will be assigned to the output\nFile object.","type":"string"},"id":{"description":"The unique identifier for this object.","type":"string"},"label":{"description":"A short, human-readable label of this object.","type":"string"},"outputBinding":{"$ref":"#/definitions/CommandOutputBinding","description":"Describes how to generate this output object based on the files produced by a CommandLineTool"},"secondaryFiles":{"anyOf":[{"$ref":"#/definitions/SecondaryFileSchema"},{"items":{"$ref":"#/definitions/SecondaryFileSchema"},"type":"array"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nProvides a pattern or expression specifying files or\ndirectories that should be included alongside the primary\nfile.  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Default: `false`.","type":"boolean"},"type":{"anyOf":[{"$ref":"#/definitions/CommandOutputArraySchema"},{"$ref":"#/definitions/CommandOutputRecordSchema"},{"$ref":"#/definitions/CommandOutputEnumSchema"},{"items":{"anyOf":[{"$ref":"#/definitions/CommandOutputArraySchema"},{"$ref":"#/definitions/CommandOutputRecordSchema"},{"$ref":"#/definitions/CommandOutputEnumSchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Specify valid types of data that may be assigned to this parameter."}},"required":["type"],"type":"object"},"CommandOutputRecordField":{"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordField","oneOf":[{"additionalProperties":false,"properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"format":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nThis is the file format that will be assigned to the output\nFile object.","type":"string"},"label":{"description":"A short, human-readable label of this object.","type":"string"},"name":{"description":"The name of the field","type":"string"},"outputBinding":{"$ref":"#/definitions/CommandOutputBinding","description":"Describes how to generate this output object based on the files\nproduced by a CommandLineTool"},"secondaryFiles":{"anyOf":[{"$ref":"#/definitions/SecondaryFileSchema"},{"items":{"$ref":"#/definitions/SecondaryFileSchema"},"type":"array"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nProvides a pattern or expression specifying files or\ndirectories that should be included alongside the primary\nfile.  Secondary files may be required or optional.  When not\nexplicitly specified, secondary files specified for `inputs`\nare required and `outputs` are optional.  An implementation\nmust include matching Files and Directories in the\n`secondaryFiles` property of the primary file.  These Files\nand Directories must be transferred and staged alongside the\nprimary file.  An implementation may fail workflow execution\nif a required secondary file does not exist.\n\nIf the value is an expression, the value of `self` in the expression\nmust be the primary input or output File object to which this binding\napplies.  The `basename`, `nameroot` and `nameext` fields must be\npresent in `self`.  For `CommandLineTool` outputs the `path` field must\nalso be present.  The expression must return a filename string relative\nto the path to the primary File, a File or Directory object with either\n`path` or `location` and `basename` fields set, or an array consisting\nof strings or File or Directory objects.  It is legal to reference an\nunchanged File or Directory object taken from input as a secondaryFile.\nThe expression may return \"null\" in which case there is no secondaryFile\nfrom that expression.\n\nTo work on non-filename-preserving storage systems, portable tool\ndescriptions should avoid constructing new values from `location`, but\nshould construct relative references using `basename` or `nameroot`\ninstead.\n\nIf a value in `secondaryFiles` is a string that is not an expression,\nit specifies that the following pattern should be applied to the path\nof the primary file to yield a filename relative to the primary File:\n\n  1. If string ends with `?` character, remove the last `?` and mark\n    the resulting secondary file as optional.\n  2. If string begins with one or more caret `^` characters, for each\n    caret, remove the last file extension from the path (the last\n    period `.` and all following characters).  If there are no file\n    extensions, the path is unchanged.\n  3. Append the remainder of the string to the end of the file path."},"streamable":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nA value of `true` indicates that the file is read or written\nsequentially without seeking.  An implementation may use this flag to\nindicate whether it is valid to stream file contents using a named\npipe.  Default: `false`.","type":"boolean"},"type":{"anyOf":[{"$ref":"#/definitions/CommandOutputArraySchema"},{"$ref":"#/definitions/CommandOutputRecordSchema"},{"$ref":"#/definitions/CommandOutputEnumSchema"},{"items":{"anyOf":[{"$ref":"#/definitions/CommandOutputArraySchema"},{"$ref":"#/definitions/CommandOutputRecordSchema"},{"$ref":"#/definitions/CommandOutputEnumSchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"The field type"}},"required":["name","type"],"type":"object"},{"type":"array","items":{"anyOf":[{"$ref":"#/definitions/CommandOutputArraySchema"},{"$ref":"#/definitions/CommandOutputRecordSchema"},{"$ref":"#/definitions/CommandOutputEnumSchema"},{"items":{"anyOf":[{"$ref":"#/definitions/CommandOutputArraySchema"},{"$ref":"#/definitions/CommandOutputRecordSchema"},{"$ref":"#/definitions/CommandOutputEnumSchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"The field type"}}]},"CommandOutputRecordSchema":{"additionalProperties":false,"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordSchema","properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"fields":{"description":"Defines the fields of the record.","oneOf":[{"items":{"$ref":"#/definitions/CommandOutputRecordField"},"type":"array"},{"patternProperties":{"^[_a-zA-Z][a-zA-Z0-9_-]*$":{"$ref":"#/definitions/CommandOutputRecordFieldMap"}},"type":"object"}]},"label":{"description":"A short, human-readable label of this object.","type":"string"},"name":{"description":"The identifier for this type","type":"string"},"type":{"const":"record","description":"Must be `record`","type":"string"}},"required":["type"],"type":"object"},"DefaultFetcher":{"additionalProperties":false,"type":"object"},"Dictionary<any>":{"additionalProperties":{"$ref":"#/definitions/T"},"type":"object"},"Dictionary<string>":{"additionalProperties":{"$ref":"#/definitions/T"},"type":"object"},"Directory":{"additionalProperties":false,"description":"Represents a directory to present to a command line tool.\n\nDirectories are represented as objects with `class` of `Directory`.  Directory objects have\na number of properties that provide metadata about the directory.\n\nThe `location` property of a Directory is a IRI that uniquely identifies\nthe directory.  Implementations must support the file:// IRI scheme and may\nsupport other schemes such as http://.  Alternately to `location`,\nimplementations must also accept the `path` property on Directory, which\nmust be a filesystem path available on the same host as the CWL runner (for\ninputs) or the runtime environment of a command line tool execution (for\ncommand line tool outputs).\n\nA Directory object may have a `listing` field.  This is a list of File and\nDirectory objects that are contained in the Directory.  For each entry in\n`listing`, the `basename` property defines the name of the File or\nSubdirectory when staged to disk.  If `listing` is not provided, the\nimplementation must have some way of fetching the Directory listing at\nruntime based on the `location` field.\n\nIf a Directory does not have `location`, it is a Directory literal.  A\nDirectory literal must provide `listing`.  Directory literals must be\ncreated on disk at runtime as needed.\n\nThe resources in a Directory literal do not need to have any implied\nrelationship in their `location`.  For example, a Directory listing may\ncontain two files located on different hosts.  It is the responsibility of\nthe runtime to ensure that those files are staged to disk appropriately.\nSecondary files associated with files in `listing` must also be staged to\nthe same Directory.\n\nWhen executing a CommandLineTool, Directories must be recursively staged\nfirst and have local values of `path` assigned.\n\nDirectory objects in CommandLineTool output must provide either a\n`location` IRI or a `path` property in the context of the tool execution\nruntime (local to the compute node, or within the executing container).\n\nAn ExpressionTool may forward file references from input to output by using\nthe same value for `location`.\n\nName conflicts (the same `basename` appearing multiple times in `listing`\nor in any entry in `secondaryFiles` in the listing) is a fatal error.","properties":{"basename":{"description":"The base name of the directory, that is, the name of the file without any\nleading directory path.  The base name must not contain a slash `/`.\n\nIf not provided, the implementation must set this field based on the\n`location` field by taking the final path component after parsing\n`location` as an IRI.  If `basename` is provided, it is not required to\nmatch the value from `location`.\n\nWhen this file is made available to a CommandLineTool, it must be named\nwith `basename`, i.e. the final component of the `path` field must match\n`basename`.","type":"string"},"class":{"const":"Directory","description":"Must be `Directory` to indicate this object describes a Directory.","type":"string"},"listing":{"description":"List of files or subdirectories contained in this directory.  The name\nof each file or subdirectory is determined by the `basename` field of\neach `File` or `Directory` object.  It is an error if a `File` shares a\n`basename` with any other entry in `listing`.  If two or more\n`Directory` object share the same `basename`, this must be treated as\nequivalent to a single subdirectory with the listings recursively\nmerged.","items":{"anyOf":[{"$ref":"#/definitions/Directory"},{"$ref":"#/definitions/File"}]},"type":"array"},"location":{"description":"An IRI that identifies the directory resource.  This may be a relative\nreference, in which case it must be resolved using the base IRI of the\ndocument.  The location may refer to a local or remote resource.  If\nthe `listing` field is not set, the implementation must use the\nlocation IRI to retrieve directory listing.  If an implementation is\nunable to retrieve the directory listing stored at a remote resource (due to\nunsupported protocol, access denied, or other issue) it must signal an\nerror.\n\nIf the `location` field is not provided, the `listing` field must be\nprovided.  The implementation must assign a unique identifier for\nthe `location` field.\n\nIf the `path` field is provided but the `location` field is not, an\nimplementation may assign the value of the `path` field to `location`,\nthen follow the rules above.","type":"string"},"path":{"description":"The local path where the Directory is made available prior to executing a\nCommandLineTool.  This must be set by the implementation.  This field\nmust not be used in any other context.  The command line tool being\nexecuted must be able to access the directory at `path` using the POSIX\n`opendir(2)` syscall.\n\nIf the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)\n(`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\\`, `\"`, `'`,\n`<space>`, `<tab>`, and `<newline>`) or characters\n[not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)\nfor [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)\nthen implementations may terminate the process with a\n`permanentFailure`.","type":"string"}},"required":["class"],"type":"object"},"Dirent":{"additionalProperties":false,"description":"Define a file or subdirectory that must be staged to a particular\nplace prior to executing the command line tool.  May be the result\nof executing an expression, such as building a configuration file\nfrom a template.\n\nUsually files are staged within the [designated output directory](#Runtime_environment).\nHowever, under certain circumstances, files may be staged at\narbitrary locations, see discussion for `entryname`.","properties":{"entry":{"description":"If the value is a string literal or an expression which evaluates to a\nstring, a new text file must be created with the string as the file contents.\n\nIf the value is an expression that evaluates to a `File` or\n`Directory` object, or an array of `File` or `Directory`\nobjects, this indicates the referenced file or directory\nshould be added to the designated output directory prior to\nexecuting the tool.\n\nIf the value is an expression that evaluates to `null`,\nnothing is added to the designated output directory, the entry\nhas no effect.\n\nIf the value is an expression that evaluates to some other\narray, number, or object not consisting of `File` or\n`Directory` objects, a new file must be created with the value\nserialized to JSON text as the file contents.  The JSON\nserialization behavior should match the behavior of string\ninterpolation of [Parameter\nreferences](#Parameter_references).","type":"string"},"entryname":{"description":"The \"target\" name of the file or subdirectory.  If `entry` is\na File or Directory, the `entryname` field overrides the value\nof `basename` of the File or Directory object.\n\n* Required when `entry` evaluates to file contents only\n* Optional when `entry` evaluates to a File or Directory object with a `basename`\n* Invalid when `entry` evaluates to an array of File or Directory objects.\n\nIf `entryname` is a relative path, it specifies a name within\nthe designated output directory.  A relative path starting\nwith `../` or that resolves to location above the designated output directory is an error.\n\nIf `entryname` is an absolute path (starts with a slash `/`)\nit is an error unless the following conditions are met:\n\n  * `DockerRequirement` is present in `requirements`\n  * The program is will run inside a software container\n  where, from the perspective of the program, the root\n  filesystem is not shared with any other user or\n  running program.\n\nIn this case, and the above conditions are met, then\n`entryname` may specify the absolute path within the container\nwhere the file or directory must be placed.","type":"string"},"writable":{"description":"If true, the File or Directory (or array of Files or\nDirectories) declared in `entry` must be writable by the tool.\n\nChanges to the file or directory must be isolated and not\nvisible by any other CommandLineTool process.  This may be\nimplemented by making a copy of the original file or\ndirectory.\n\nDisruptive changes to the referenced file or directory must not\nbe allowed unless `InplaceUpdateRequirement.inplaceUpdate` is true.\n\nDefault false (files and directories read-only by default).\n\nA directory marked as `writable: true` implies that all files and\nsubdirectories are recursively writable as well.\n\nIf `writable` is false, the file may be made available using a\nbind mount or file system link to avoid unnecessary copying of\nthe input file.  Command line tools may receive an error on\nattempting to rename or delete files or directories that are\nnot explicitly marked as writable.","type":"boolean"}},"required":["entry"],"type":"object"},"DockerRequirement":{"additionalProperties":false,"description":"Indicates that a workflow component should be run in a\n[Docker](https://docker.com) or Docker-compatible (such as\n[Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment and\nspecifies how to fetch or build the image.\n\nIf a CommandLineTool lists `DockerRequirement` under\n`hints` (or `requirements`), it may (or must) be run in the specified Docker\ncontainer.\n\nThe platform must first acquire or install the correct Docker image as\nspecified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`.\n\nThe platform must execute the tool in the container using `docker run` with\nthe appropriate Docker image and tool command line.\n\nThe workflow platform may provide input files and the designated output\ndirectory through the use of volume bind mounts.  The platform should rewrite\nfile paths in the input object to correspond to the Docker bind mounted\nlocations. That is, the platform should rewrite values in the parameter context\nsuch as `runtime.outdir`, `runtime.tmpdir` and others to be valid paths\nwithin the container. The platform must ensure that `runtime.outdir` and\n`runtime.tmpdir` are distinct directories.\n\nWhen running a tool contained in Docker, the workflow platform must not\nassume anything about the contents of the Docker container, such as the\npresence or absence of specific software, except to assume that the\ngenerated command line represents a valid command within the runtime\nenvironment of the container.\n\nA container image may specify an\n[ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint)\nand/or\n[CMD](https://docs.docker.com/engine/reference/builder/#cmd).\nCommand line arguments will be appended after all elements of\nENTRYPOINT, and will override all elements specified using CMD (in\nother words, CMD is only used when the CommandLineTool definition\nproduces an empty command line).\n\nUse of implicit ENTRYPOINT or CMD are discouraged due to reproducibility\nconcerns of the implicit hidden execution point (For further discussion, see\n[https://doi.org/10.12688/f1000research.15140.1](https://doi.org/10.12688/f1000research.15140.1)). Portable\nCommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD.\nCommandLineTools which do rely on ENTRYPOINT or CMD must list `DockerRequirement` in the\n`requirements` section.\n\n## Interaction with other requirements\n\nIf [EnvVarRequirement](#EnvVarRequirement) is specified alongside a\nDockerRequirement, the environment variables must be provided to Docker\nusing `--env` or `--env-file` and interact with the container's preexisting\nenvironment as defined by Docker.","properties":{"class":{"const":"DockerRequirement","description":"Always 'DockerRequirement'","type":"string"},"dockerFile":{"description":"Supply the contents of a Dockerfile which will be built using `docker build`.","type":"string"},"dockerImageId":{"description":"The image id that will be used for `docker run`.  May be a\nhuman-readable image name or the image identifier hash.  May be skipped\nif `dockerPull` is specified, in which case the `dockerPull` image id\nmust be used.","type":"string"},"dockerImport":{"description":"Provide HTTP URL to download and gunzip a Docker images using `docker import.","type":"string"},"dockerLoad":{"description":"Specify an HTTP URL from which to download a Docker image using `docker load`.","type":"string"},"dockerOutputDirectory":{"description":"Set the designated output directory to a specific location inside the\nDocker container.","type":"string"},"dockerPull":{"description":"Specify a Docker image to retrieve using `docker pull`. Can contain the\nimmutable digest to ensure an exact container is used:\n`dockerPull: ubuntu@sha256:45b23dee08af5e43a7fea6c4cf9c25ccf269ee113168c19722f87876677c5cb2`","type":"string"}},"required":["class"],"type":"object"},"EnvVarRequirement":{"additionalProperties":false,"description":"Define a list of environment variables which will be set in the\nexecution environment of the tool.  See `EnvironmentDef` for details.","properties":{"class":{"const":"EnvVarRequirement","description":"Always 'EnvVarRequirement'","type":"string"},"envDef":{"description":"The list of environment variables.","oneOf":[{"items":{"anyOf":[{"$ref":"#/definitions/EnvironmentDef"},{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"}]},"type":"array"},{"patternProperties":{"^[_a-zA-Z][a-zA-Z0-9_-]*$":{"type":"string"}}}]}},"required":["class","envDef"],"type":"object"},"EnvironmentDef":{"additionalProperties":false,"description":"Define an environment variable that will be set in the runtime environment\nby the workflow platform when executing the command line tool.  May be the\nresult of executing an expression, such as getting a parameter from input.","properties":{"envName":{"description":"The environment variable name","type":"string"},"envValue":{"description":"The environment variable value","type":"string"}},"required":["envName","envValue"],"type":"object"},"ExpressionTool":{"description":"An ExpressionTool is a type of Process object that can be run by itself\nor as a Workflow step. It executes a pure Javascript expression that has\naccess to the same input parameters as a workflow. It is meant to be used\nsparingly as a way to isolate complex Javascript expressions that need to\noperate on input data and produce some result; perhaps just a\nrearrangement of the inputs. No Docker software container is required\nor allowed.","properties":{"class":{"const":"ExpressionTool","type":"string"},"cwlVersion":{"description":"CWL document version. Always required at the document root. Not\nrequired for a Process embedded inside another Process.","enum":["draft-2","draft-3","draft-3.dev1","draft-3.dev2","draft-3.dev3","draft-3.dev4","draft-3.dev5","draft-4.dev1","draft-4.dev2","draft-4.dev3","v1.0","v1.0.dev4","v1.1","v1.1.0-dev1","v1.2","v1.2.0-dev1","v1.2.0-dev2","v1.2.0-dev3","v1.2.0-dev4","v1.2.0-dev5"],"type":"string"},"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"expression":{"description":"The expression to execute.  The expression must return a plain\nJavascript object which matches the output parameters of the\nExpressionTool.","type":"string"},"hints":{"description":"Declares requirements that apply to either the runtime environment or the\nworkflow engine that must be met in order to execute this process.  If\nan implementation cannot satisfy all requirements, or a requirement is\nlisted which is not recognized by the implementation, it is a fatal\nerror and the implementation must not attempt to run the process,\nunless overridden at user option.","oneOf":[{"items":{"anyOf":[{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"},{"$ref":"#/definitions/InlineJavascriptRequirement"},{"$ref":"#/definitions/SchemaDefRequirement"},{"$ref":"#/definitions/LoadListingRequirement"},{"$ref":"#/definitions/DockerRequirement"},{"$ref":"#/definitions/SoftwareRequirement"},{"$ref":"#/definitions/InitialWorkDirRequirement"},{"$ref":"#/definitions/EnvVarRequirement"},{"$ref":"#/definitions/ShellCommandRequirement"},{"$ref":"#/definitions/ResourceRequirement"},{"$ref":"#/definitions/WorkReuse"},{"$ref":"#/definitions/NetworkAccess"},{"$ref":"#/definitions/InplaceUpdateRequirement"},{"$ref":"#/definitions/ToolTimeLimit"},{"$ref":"#/definitions/SubworkflowFeatureRequirement"},{"$ref":"#/definitions/ScatterFeatureRequirement"},{"$ref":"#/definitions/MultipleInputFeatureRequirement"},{"$ref":"#/definitions/StepInputExpressionRequirement"}]},"type":"array"},{"type":"object","properties":{"InlineJavascriptRequirement":{"anyOf":[{"$ref":"#/definitions/InlineJavascriptRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SchemaDefRequirement":{"anyOf":[{"$ref":"#/definitions/SchemaDefRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"LoadListingRequirement":{"anyOf":[{"$ref":"#/definitions/LoadListingRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"DockerRequirement":{"anyOf":[{"$ref":"#/definitions/DockerRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SoftwareRequirement":{"anyOf":[{"$ref":"#/definitions/SoftwareRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"InitialWorkDirRequirement":{"anyOf":[{"$ref":"#/definitions/InitialWorkDirRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"EnvVarRequirement":{"anyOf":[{"$ref":"#/definitions/EnvVarRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ShellCommandRequirement":{"anyOf":[{"$ref":"#/definitions/ShellCommandRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ResourceRequirement":{"anyOf":[{"$ref":"#/definitions/ResourceRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"WorkReuse":{"anyOf":[{"$ref":"#/definitions/WorkReuseMap"},{"type":"object","properties":{},"additionalProperties":false}]},"NetworkAccess":{"anyOf":[{"$ref":"#/definitions/NetworkAccessMap"},{"type":"object","properties":{},"additionalProperties":false}]},"InplaceUpdateRequirement":{"anyOf":[{"$ref":"#/definitions/InplaceUpdateRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ToolTimeLimit":{"anyOf":[{"$ref":"#/definitions/ToolTimeLimitMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SubworkflowFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/SubworkflowFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ScatterFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/ScatterFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"MultipleInputFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/MultipleInputFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"StepInputExpressionRequirement":{"anyOf":[{"$ref":"#/definitions/StepInputExpressionRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]}},"additionalProperties":false}]},"id":{"description":"The unique identifier for this object.\n\nOnly useful for `$graph` at `Process` level. Should not be exposed\nto users in graphical or terminal user interfaces.","type":"string"},"inputs":{"description":"Defines the input parameters of the process.  The process is ready to\nrun when all required input parameters are associated with concrete\nvalues.  Input parameters include a schema for each parameter which is\nused to validate the input object.  It may also be used to build a user\ninterface for constructing the input object.\n\nWhen accepting an input object, all input parameters must have a value.\nIf an input parameter is missing from the input object, it must be\nassigned a value of `null` (or the value of `default` for that\nparameter, if provided) for the purposes of validation and evaluation\nof expressions.","oneOf":[{"items":{"$ref":"#/definitions/WorkflowInputParameter"},"type":"array"},{"patternProperties":{"^[_a-zA-Z][a-zA-Z0-9_-]*$":{"oneOf":[{"$ref":"#/definitions/WorkflowInputParameter"},{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Specify valid types of data that may be assigned to this parameter."},{"type":"array","items":{"oneOf":[{"type":"string"},{"$ref":"#/definitions/WorkflowInputParameter"}]}}]}},"type":"object"}]},"intent":{"description":"An identifier for the type of computational operation, of this Process.\nEspecially useful for [`Operation`](Workflow.html#Operation), but can also be used for\n[`CommandLineTool`](CommandLineTool.html#CommandLineTool),\n[`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool).\n\nIf provided, then this must be an IRI of a concept node that\nrepresents the type of operation, preferably defined within an ontology.\n\nFor example, in the domain of bioinformatics, one can use an IRI from\nthe EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004),\nlike [Alignment](http://edamontology.org/operation_2928),\nor [Clustering](http://edamontology.org/operation_3432); or a more\nspecific Operation concept like\n[Split read mapping](http://edamontology.org/operation_3199).","items":{"type":"string"},"type":"array"},"label":{"description":"A short, human-readable label of this object.","type":"string"},"outputs":{"description":"Defines the parameters representing the output of the process.  May be\nused to generate and/or validate the output object.","oneOf":[{"items":{"$ref":"#/definitions/ExpressionToolOutputParameter"},"type":"array"},{"patternProperties":{"^[_a-zA-Z][a-zA-Z0-9_-]*$":{"oneOf":[{"$ref":"#/definitions/ExpressionToolOutputParameter"},{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Specify valid types of data that may be assigned to this parameter.\nNote that this field just acts as a hint, as the outputs of an\nExpressionTool process are always considered valid."},{"type":"array","items":{"oneOf":[{"type":"string"},{"$ref":"#/definitions/ExpressionToolOutputParameter"}]}}]}},"type":"object"}]},"requirements":{"description":"Declares requirements that apply to either the runtime environment or the\nworkflow engine that must be met in order to execute this process.  If\nan implementation cannot satisfy all requirements, or a requirement is\nlisted which is not recognized by the implementation, it is a fatal\nerror and the implementation must not attempt to run the process,\nunless overridden at user option.","oneOf":[{"items":{"anyOf":[{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"},{"$ref":"#/definitions/InlineJavascriptRequirement"},{"$ref":"#/definitions/SchemaDefRequirement"},{"$ref":"#/definitions/LoadListingRequirement"},{"$ref":"#/definitions/DockerRequirement"},{"$ref":"#/definitions/SoftwareRequirement"},{"$ref":"#/definitions/InitialWorkDirRequirement"},{"$ref":"#/definitions/EnvVarRequirement"},{"$ref":"#/definitions/ShellCommandRequirement"},{"$ref":"#/definitions/ResourceRequirement"},{"$ref":"#/definitions/WorkReuse"},{"$ref":"#/definitions/NetworkAccess"},{"$ref":"#/definitions/InplaceUpdateRequirement"},{"$ref":"#/definitions/ToolTimeLimit"},{"$ref":"#/definitions/SubworkflowFeatureRequirement"},{"$ref":"#/definitions/ScatterFeatureRequirement"},{"$ref":"#/definitions/MultipleInputFeatureRequirement"},{"$ref":"#/definitions/StepInputExpressionRequirement"}]},"type":"array"},{"type":"object","properties":{"InlineJavascriptRequirement":{"anyOf":[{"$ref":"#/definitions/InlineJavascriptRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SchemaDefRequirement":{"anyOf":[{"$ref":"#/definitions/SchemaDefRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"LoadListingRequirement":{"anyOf":[{"$ref":"#/definitions/LoadListingRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"DockerRequirement":{"anyOf":[{"$ref":"#/definitions/DockerRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SoftwareRequirement":{"anyOf":[{"$ref":"#/definitions/SoftwareRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"InitialWorkDirRequirement":{"anyOf":[{"$ref":"#/definitions/InitialWorkDirRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"EnvVarRequirement":{"anyOf":[{"$ref":"#/definitions/EnvVarRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ShellCommandRequirement":{"anyOf":[{"$ref":"#/definitions/ShellCommandRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ResourceRequirement":{"anyOf":[{"$ref":"#/definitions/ResourceRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"WorkReuse":{"anyOf":[{"$ref":"#/definitions/WorkReuseMap"},{"type":"object","properties":{},"additionalProperties":false}]},"NetworkAccess":{"anyOf":[{"$ref":"#/definitions/NetworkAccessMap"},{"type":"object","properties":{},"additionalProperties":false}]},"InplaceUpdateRequirement":{"anyOf":[{"$ref":"#/definitions/InplaceUpdateRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ToolTimeLimit":{"anyOf":[{"$ref":"#/definitions/ToolTimeLimitMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SubworkflowFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/SubworkflowFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ScatterFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/ScatterFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"MultipleInputFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/MultipleInputFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"StepInputExpressionRequirement":{"anyOf":[{"$ref":"#/definitions/StepInputExpressionRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]}},"additionalProperties":false}]}},"required":["class","expression","inputs","outputs"],"type":"object"},"ExpressionToolOutputParameter":{"additionalProperties":false,"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#ExpressionToolOutputParameter","properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"format":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nThis is the file format that will be assigned to the output\nFile object.","type":"string"},"id":{"description":"The unique identifier for this object.","type":"string"},"label":{"description":"A short, human-readable label of this object.","type":"string"},"secondaryFiles":{"anyOf":[{"$ref":"#/definitions/SecondaryFileSchema"},{"items":{"$ref":"#/definitions/SecondaryFileSchema"},"type":"array"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nProvides a pattern or expression specifying files or\ndirectories that should be included alongside the primary\nfile.  Secondary files may be required or optional.  When not\nexplicitly specified, secondary files specified for `inputs`\nare required and `outputs` are optional.  An implementation\nmust include matching Files and Directories in the\n`secondaryFiles` property of the primary file.  These Files\nand Directories must be transferred and staged alongside the\nprimary file.  An implementation may fail workflow execution\nif a required secondary file does not exist.\n\nIf the value is an expression, the value of `self` in the expression\nmust be the primary input or output File object to which this binding\napplies.  The `basename`, `nameroot` and `nameext` fields must be\npresent in `self`.  For `CommandLineTool` outputs the `path` field must\nalso be present.  The expression must return a filename string relative\nto the path to the primary File, a File or Directory object with either\n`path` or `location` and `basename` fields set, or an array consisting\nof strings or File or Directory objects.  It is legal to reference an\nunchanged File or Directory object taken from input as a secondaryFile.\nThe expression may return \"null\" in which case there is no secondaryFile\nfrom that expression.\n\nTo work on non-filename-preserving storage systems, portable tool\ndescriptions should avoid constructing new values from `location`, but\nshould construct relative references using `basename` or `nameroot`\ninstead.\n\nIf a value in `secondaryFiles` is a string that is not an expression,\nit specifies that the following pattern should be applied to the path\nof the primary file to yield a filename relative to the primary File:\n\n  1. If string ends with `?` character, remove the last `?` and mark\n    the resulting secondary file as optional.\n  2. If string begins with one or more caret `^` characters, for each\n    caret, remove the last file extension from the path (the last\n    period `.` and all following characters).  If there are no file\n    extensions, the path is unchanged.\n  3. Append the remainder of the string to the end of the file path."},"streamable":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nA value of `true` indicates that the file is read or written\nsequentially without seeking.  An implementation may use this flag to\nindicate whether it is valid to stream file contents using a named\npipe.  Default: `false`.","type":"boolean"},"type":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Specify valid types of data that may be assigned to this parameter.\nNote that this field just acts as a hint, as the outputs of an\nExpressionTool process are always considered valid."}},"required":["type"],"type":"object"},"Fetcher":{"oneOf":[{"$ref":"#/definitions/DefaultFetcher"}]},"File":{"additionalProperties":false,"description":"Represents a file (or group of files when `secondaryFiles` is provided) that\nwill be accessible by tools using standard POSIX file system call API such as\nopen(2) and read(2).\n\nFiles are represented as objects with `class` of `File`.  File objects have\na number of properties that provide metadata about the file.\n\nThe `location` property of a File is a IRI that uniquely identifies the\nfile.  Implementations must support the `file://` IRI scheme and may support\nother schemes such as `http://` and `https://`.  The value of `location` may also be a\nrelative reference, in which case it must be resolved relative to the IRI\nof the document it appears in.  Alternately to `location`, implementations\nmust also accept the `path` property on File, which must be a filesystem\npath available on the same host as the CWL runner (for inputs) or the\nruntime environment of a command line tool execution (for command line tool\noutputs).\n\nIf no `location` or `path` is specified, a file object must specify\n`contents` with the UTF-8 text content of the file.  This is a \"file\nliteral\".  File literals do not correspond to external resources, but are\ncreated on disk with `contents` with when needed for executing a tool.\nWhere appropriate, expressions can return file literals to define new files\non a runtime.  The maximum size of `contents` is 64 kilobytes.\n\nThe `basename` property defines the filename on disk where the file is\nstaged.  This may differ from the resource name.  If not provided,\n`basename` must be computed from the last path part of `location` and made\navailable to expressions.\n\nThe `secondaryFiles` property is a list of File or Directory objects that\nmust be staged in the same directory as the primary file.  It is an error\nfor file names to be duplicated in `secondaryFiles`.\n\nThe `size` property is the size in bytes of the File.  It must be computed\nfrom the resource and made available to expressions.  The `checksum` field\ncontains a cryptographic hash of the file content for use it verifying file\ncontents.  Implementations may, at user option, enable or disable\ncomputation of the `checksum` field for performance or other reasons.\nHowever, the ability to compute output checksums is required to pass the\nCWL conformance test suite.\n\nWhen executing a CommandLineTool, the files and secondary files may be\nstaged to an arbitrary directory, but must use the value of `basename` for\nthe filename.  The `path` property must be file path in the context of the\ntool execution runtime (local to the compute node, or within the executing\ncontainer).  All computed properties should be available to expressions.\nFile literals also must be staged and `path` must be set.\n\nWhen collecting CommandLineTool outputs, `glob` matching returns file paths\n(with the `path` property) and the derived properties. This can all be\nmodified by `outputEval`.  Alternately, if the file `cwl.output.json` is\npresent in the output, `outputBinding` is ignored.\n\nFile objects in the output must provide either a `location` IRI or a `path`\nproperty in the context of the tool execution runtime (local to the compute\nnode, or within the executing container).\n\nWhen evaluating an ExpressionTool, file objects must be referenced via\n`location` (the expression tool does not have access to files on disk so\n`path` is meaningless) or as file literals.  It is legal to return a file\nobject with an existing `location` but a different `basename`.  The\n`loadContents` field of ExpressionTool inputs behaves the same as on\nCommandLineTool inputs, however it is not meaningful on the outputs.\n\nAn ExpressionTool may forward file references from input to output by using\nthe same value for `location`.","properties":{"basename":{"description":"The base name of the file, that is, the name of the file without any\nleading directory path.  The base name must not contain a slash `/`.\n\nIf not provided, the implementation must set this field based on the\n`location` field by taking the final path component after parsing\n`location` as an IRI.  If `basename` is provided, it is not required to\nmatch the value from `location`.\n\nWhen this file is made available to a CommandLineTool, it must be named\nwith `basename`, i.e. the final component of the `path` field must match\n`basename`.","type":"string"},"checksum":{"description":"Optional hash code for validating file integrity.  Currently, must be in the form\n\"sha1$ + hexadecimal string\" using the SHA-1 algorithm.","type":"string"},"class":{"const":"File","description":"Must be `File` to indicate this object describes a file.","type":"string"},"contents":{"description":"File contents literal.\n\nIf neither `location` nor `path` is provided, `contents` must be\nnon-null.  The implementation must assign a unique identifier for the\n`location` field.  When the file is staged as input to CommandLineTool,\nthe value of `contents` must be written to a file.\n\nIf `contents` is set as a result of a Javascript expression,\nan `entry` in `InitialWorkDirRequirement`, or read in from\n`cwl.output.json`, there is no specified upper limit on the\nsize of `contents`.  Implementations may have practical limits\non the size of `contents` based on memory and storage\navailable to the workflow runner or other factors.\n\nIf the `loadContents` field of an `InputParameter` or\n`OutputParameter` is true, and the input or output File object\n`location` is valid, the file must be a UTF-8 text file 64 KiB\nor smaller, and the implementation must read the entire\ncontents of the file and place it in the `contents` field.  If\nthe size of the file is greater than 64 KiB, the\nimplementation must raise a fatal error.","type":"string"},"dirname":{"description":"The name of the directory containing file, that is, the path leading up\nto the final slash in the path such that `dirname + '/' + basename ==\npath`.\n\nThe implementation must set this field based on the value of `path`\nprior to evaluating parameter references or expressions in a\nCommandLineTool document.  This field must not be used in any other\ncontext.","type":"string"},"format":{"description":"The format of the file: this must be an IRI of a concept node that\nrepresents the file format, preferably defined within an ontology.\nIf no ontology is available, file formats may be tested by exact match.\n\nReasoning about format compatibility must be done by checking that an\ninput file format is the same, `owl:equivalentClass` or\n`rdfs:subClassOf` the format required by the input parameter.\n`owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if\n`<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer\n`<C> owl:subclassOf <A>`.\n\nFile format ontologies may be provided in the \"$schemas\" metadata at the\nroot of the document.  If no ontologies are specified in `$schemas`, the\nruntime may perform exact file format matches.","type":"string"},"location":{"description":"An IRI that identifies the file resource.  This may be a relative\nreference, in which case it must be resolved using the base IRI of the\ndocument.  The location may refer to a local or remote resource; the\nimplementation must use the IRI to retrieve file content.  If an\nimplementation is unable to retrieve the file content stored at a\nremote resource (due to unsupported protocol, access denied, or other\nissue) it must signal an error.\n\nIf the `location` field is not provided, the `contents` field must be\nprovided.  The implementation must assign a unique identifier for\nthe `location` field.\n\nIf the `path` field is provided but the `location` field is not, an\nimplementation may assign the value of the `path` field to `location`,\nthen follow the rules above.","type":"string"},"nameext":{"description":"The basename extension such that `nameroot + nameext == basename`, and\n`nameext` is empty or begins with a period and contains at most one\nperiod.  Leading periods on the basename are ignored; a basename of\n`.cshrc` will have an empty `nameext`.\n\nThe implementation must set this field automatically based on the value\nof `basename` prior to evaluating parameter references or expressions.","type":"string"},"nameroot":{"description":"The basename root such that `nameroot + nameext == basename`, and\n`nameext` is empty or begins with a period and contains at most one\nperiod.  For the purposes of path splitting leading periods on the\nbasename are ignored; a basename of `.cshrc` will have a nameroot of\n`.cshrc`.\n\nThe implementation must set this field automatically based on the value\nof `basename` prior to evaluating parameter references or expressions.","type":"string"},"path":{"description":"The local host path where the File is available when a CommandLineTool is\nexecuted.  This field must be set by the implementation.  The final\npath component must match the value of `basename`.  This field\nmust not be used in any other context.  The command line tool being\nexecuted must be able to access the file at `path` using the POSIX\n`open(2)` syscall.\n\nAs a special case, if the `path` field is provided but the `location`\nfield is not, an implementation may assign the value of the `path`\nfield to `location`, and remove the `path` field.\n\nIf the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)\n(`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\\`, `\"`, `'`,\n`<space>`, `<tab>`, and `<newline>`) or characters\n[not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)\nfor [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)\nthen implementations may terminate the process with a\n`permanentFailure`.","type":"string"},"secondaryFiles":{"description":"A list of additional files or directories that are associated with the\nprimary file and must be transferred alongside the primary file.\nExamples include indexes of the primary file, or external references\nwhich must be included when loading primary document.  A file object\nlisted in `secondaryFiles` may itself include `secondaryFiles` for\nwhich the same rules apply.","items":{"anyOf":[{"$ref":"#/definitions/Directory"},{"$ref":"#/definitions/File"}]},"type":"array"},"size":{"description":"Optional file size (in bytes)","type":"number"}},"required":["class"],"type":"object"},"InitialWorkDirRequirement":{"additionalProperties":false,"description":"Define a list of files and subdirectories that must be staged by the workflow platform prior to executing the command line tool.\nNormally files are staged within the designated output directory. However, when running inside containers, files may be staged at arbitrary locations, see discussion for [`Dirent.entryname`](#Dirent). Together with `DockerRequirement.dockerOutputDirectory` it is possible to control the locations of both input and output files when running in containers.","properties":{"class":{"const":"InitialWorkDirRequirement","description":"InitialWorkDirRequirement","type":"string"},"listing":{"anyOf":[{"items":{"anyOf":[{"anyOf":[{"$ref":"#/definitions/Directory"},{"$ref":"#/definitions/File"},{"items":{"anyOf":[{"anyOf":[{"$ref":"#/definitions/Directory"},{"$ref":"#/definitions/File"}]},{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"}]},"type":"array"},{"$ref":"#/definitions/Dirent"},{"type":"string"}]},{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"}]},"type":"array"},{"type":"string"}],"description":"The list of files or subdirectories that must be staged prior\nto executing the command line tool.\n\nReturn type of each expression must validate as `[\"null\",\nFile, Directory, Dirent, {type: array, items: [File,\nDirectory]}]`.\n\nEach `File` or `Directory` that is returned by an Expression\nmust be added to the designated output directory prior to\nexecuting the tool.\n\nEach `Dirent` record that is listed or returned by an\nexpression specifies a file to be created or staged in the\ndesignated output directory prior to executing the tool.\n\nExpressions may return null, in which case they have no effect.\n\nFiles or Directories which are listed in the input parameters\nand appear in the `InitialWorkDirRequirement` listing must\nhave their `path` set to their staged location.  If the same\nFile or Directory appears more than once in the\n`InitialWorkDirRequirement` listing, the implementation must\nchoose exactly one value for `path`; how this value is chosen\nis undefined."}},"required":["class"],"type":"object"},"InlineJavascriptRequirement":{"additionalProperties":false,"description":"Indicates that the workflow platform must support inline Javascript expressions.\nIf this requirement is not present, the workflow platform must not perform expression\ninterpolation.","properties":{"class":{"const":"InlineJavascriptRequirement","description":"Always 'InlineJavascriptRequirement'","type":"string"},"expressionLib":{"description":"Additional code fragments that will also be inserted\nbefore executing the expression code.  Allows for function definitions that may\nbe called from CWL expressions.","items":{"anyOf":[{"type":"string"},{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"}]},"type":"array"}},"required":["class"],"type":"object"},"InplaceUpdateRequirement":{"additionalProperties":false,"description":"\nIf `inplaceUpdate` is true, then an implementation supporting this\nfeature may permit tools to directly update files with `writable:\ntrue` in InitialWorkDirRequirement.  That is, as an optimization,\nfiles may be destructively modified in place as opposed to copied\nand updated.\n\nAn implementation must ensure that only one workflow step may\naccess a writable file at a time.  It is an error if a file which\nis writable by one workflow step file is accessed (for reading or\nwriting) by any other workflow step running independently.\nHowever, a file which has been updated in a previous completed\nstep may be used as input to multiple steps, provided it is\nread-only in every step.\n\nWorkflow steps which modify a file must produce the modified file\nas output.  Downstream steps which further process the file must\nuse the output of previous steps, and not refer to a common input\n(this is necessary for both ordering and correctness).\n\nWorkflow authors should provide this in the `hints` section.  The\nintent of this feature is that workflows produce the same results\nwhether or not InplaceUpdateRequirement is supported by the\nimplementation, and this feature is primarily available as an\noptimization for particular environments.\n\nUsers and implementers should be aware that workflows that\ndestructively modify inputs may not be repeatable or reproducible.\nIn particular, enabling this feature implies that WorkReuse should\nnot be enabled.","properties":{"class":{"const":"InplaceUpdateRequirement","description":"Always 'InplaceUpdateRequirement'","type":"string"},"inplaceUpdate":{"type":"boolean"}},"required":["class","inplaceUpdate"],"type":"object"},"InputArraySchema":{"additionalProperties":false,"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#InputArraySchema","properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"items":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Defines the type of the array elements."},"label":{"description":"A short, human-readable label of this object.","type":"string"},"name":{"description":"The identifier for this type","type":"string"},"type":{"const":"array","description":"Must be `array`","type":"string"}},"required":["items","type"],"type":"object"},"InputBinding":{"additionalProperties":false,"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#InputBinding","properties":{"loadContents":{"description":"Use of `loadContents` in `InputBinding` is deprecated.\nPreserved for v1.0 backwards compatibility.  Will be removed in\nCWL v2.0.  Use `InputParameter.loadContents` instead.","type":"boolean"}},"required":[],"type":"object"},"InputEnumSchema":{"additionalProperties":false,"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#InputEnumSchema","properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"label":{"description":"A short, human-readable label of this object.","type":"string"},"name":{"description":"The identifier for this type","type":"string"},"symbols":{"description":"Defines the set of valid symbols.","items":{"type":"string"},"type":"array"},"type":{"const":"enum","description":"Must be `enum`","type":"string"}},"required":["symbols","type"],"type":"object"},"InputRecordField":{"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordField","oneOf":[{"additionalProperties":false,"properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"format":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nThis must be one or more IRIs of concept nodes\nthat represents file formats which are allowed as input to this\nparameter, preferably defined within an ontology.  If no ontology is\navailable, file formats may be tested by exact match."},"label":{"description":"A short, human-readable label of this object.","type":"string"},"loadContents":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nIf true, the file (or each file in the array) must be a UTF-8\ntext file 64 KiB or smaller, and the implementation must read\nthe entire contents of the file (or file array) and place it\nin the `contents` field of the File object for use by\nexpressions.  If the size of the file is greater than 64 KiB,\nthe implementation must raise a fatal error.","type":"boolean"},"loadListing":{"description":"Only valid when `type: Directory` or is an array of `items: Directory`.\n\nSpecify the desired behavior for loading the `listing` field of\na Directory object for use by expressions.\n\nThe order of precedence for loadListing is:\n\n  1. `loadListing` on an individual parameter\n  2. Inherited from `LoadListingRequirement`\n  3. By default: `no_listing`","enum":["deep_listing","no_listing","shallow_listing"],"type":"string"},"name":{"description":"The name of the field","type":"string"},"secondaryFiles":{"anyOf":[{"$ref":"#/definitions/SecondaryFileSchema"},{"items":{"$ref":"#/definitions/SecondaryFileSchema"},"type":"array"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nProvides a pattern or expression specifying files or\ndirectories that should be included alongside the primary\nfile.  Secondary files may be required or optional.  When not\nexplicitly specified, secondary files specified for `inputs`\nare required and `outputs` are optional.  An implementation\nmust include matching Files and Directories in the\n`secondaryFiles` property of the primary file.  These Files\nand Directories must be transferred and staged alongside the\nprimary file.  An implementation may fail workflow execution\nif a required secondary file does not exist.\n\nIf the value is an expression, the value of `self` in the expression\nmust be the primary input or output File object to which this binding\napplies.  The `basename`, `nameroot` and `nameext` fields must be\npresent in `self`.  For `CommandLineTool` outputs the `path` field must\nalso be present.  The expression must return a filename string relative\nto the path to the primary File, a File or Directory object with either\n`path` or `location` and `basename` fields set, or an array consisting\nof strings or File or Directory objects.  It is legal to reference an\nunchanged File or Directory object taken from input as a secondaryFile.\nThe expression may return \"null\" in which case there is no secondaryFile\nfrom that expression.\n\nTo work on non-filename-preserving storage systems, portable tool\ndescriptions should avoid constructing new values from `location`, but\nshould construct relative references using `basename` or `nameroot`\ninstead.\n\nIf a value in `secondaryFiles` is a string that is not an expression,\nit specifies that the following pattern should be applied to the path\nof the primary file to yield a filename relative to the primary File:\n\n  1. If string ends with `?` character, remove the last `?` and mark\n    the resulting secondary file as optional.\n  2. If string begins with one or more caret `^` characters, for each\n    caret, remove the last file extension from the path (the last\n    period `.` and all following characters).  If there are no file\n    extensions, the path is unchanged.\n  3. Append the remainder of the string to the end of the file path."},"streamable":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nA value of `true` indicates that the file is read or written\nsequentially without seeking.  An implementation may use this flag to\nindicate whether it is valid to stream file contents using a named\npipe.  Default: `false`.","type":"boolean"},"type":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"The field type"}},"required":["name","type"],"type":"object"},{"type":"array","items":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"The field type"}}]},"InputRecordSchema":{"additionalProperties":false,"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordSchema","properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"fields":{"description":"Defines the fields of the record.","oneOf":[{"items":{"$ref":"#/definitions/InputRecordField"},"type":"array"},{"patternProperties":{"^[_a-zA-Z][a-zA-Z0-9_-]*$":{"$ref":"#/definitions/InputRecordFieldMap"}},"type":"object"}]},"label":{"description":"A short, human-readable label of this object.","type":"string"},"name":{"description":"The identifier for this type","type":"string"},"type":{"const":"record","description":"Must be `record`","type":"string"}},"required":["type"],"type":"object"},"LoadListingRequirement":{"additionalProperties":false,"description":"Specify the desired behavior for loading the `listing` field of\na Directory object for use by expressions.","properties":{"class":{"const":"LoadListingRequirement","description":"Always 'LoadListingRequirement'","type":"string"},"loadListing":{"enum":["deep_listing","no_listing","shallow_listing"],"type":"string"}},"required":["class"],"type":"object"},"LoadingOptions":{"additionalProperties":false,"properties":{"container":{"type":"string"},"copyFrom":{"$ref":"#/definitions/LoadingOptions"},"fetcher":{"$ref":"#/definitions/Fetcher"},"fileUri":{"type":"string"},"idx":{"$ref":"#/definitions/Dictionary<any>"},"namespaces":{"$ref":"#/definitions/Dictionary<string>"},"noLinkCheck":{"type":"boolean"},"originalDoc":{},"rvocab":{"$ref":"#/definitions/Dictionary<string>"},"schemas":{"$ref":"#/definitions/Dictionary<string>"},"vocab":{"$ref":"#/definitions/Dictionary<string>"}},"required":["fetcher","idx","originalDoc","rvocab","vocab"],"type":"object"},"MultipleInputFeatureRequirement":{"additionalProperties":false,"description":"Indicates that the workflow platform must support multiple inbound data links\nlisted in the `source` field of [WorkflowStepInput](#WorkflowStepInput).","properties":{"class":{"const":"MultipleInputFeatureRequirement","description":"Always 'MultipleInputFeatureRequirement'","type":"string"}},"required":["class"],"type":"object"},"NetworkAccess":{"additionalProperties":false,"description":"Indicate whether a process requires outgoing IPv4/IPv6 network\naccess.  Choice of IPv4 or IPv6 is implementation and site\nspecific, correct tools must support both.\n\nIf `networkAccess` is false or not specified, tools must not\nassume network access, except for localhost (the loopback device).\n\nIf `networkAccess` is true, the tool must be able to make outgoing\nconnections to network resources.  Resources may be on a private\nsubnet or the public Internet.  However, implementations and sites\nmay apply their own security policies to restrict what is\naccessible by the tool.\n\nEnabling network access does not imply a publicly routable IP\naddress or the ability to accept inbound connections.","properties":{"class":{"const":"NetworkAccess","description":"Always 'NetworkAccess'","type":"string"},"networkAccess":{"type":["string","boolean"]}},"required":["class","networkAccess"],"type":"object"},"Operation":{"additionalProperties":false,"description":"This record describes an abstract operation.  It is a potential\nstep of a workflow that has not yet been bound to a concrete\nimplementation.  It specifies an input and output signature, but\ndoes not provide enough information to be executed.  An\nimplementation (or other tooling) may provide a means of binding\nan Operation to a concrete process (such as Workflow,\nCommandLineTool, or ExpressionTool) with a compatible signature.","properties":{"class":{"const":"Operation","type":"string"},"cwlVersion":{"description":"CWL document version. Always required at the document root. Not\nrequired for a Process embedded inside another Process.","enum":["draft-2","draft-3","draft-3.dev1","draft-3.dev2","draft-3.dev3","draft-3.dev4","draft-3.dev5","draft-4.dev1","draft-4.dev2","draft-4.dev3","v1.0","v1.0.dev4","v1.1","v1.1.0-dev1","v1.2","v1.2.0-dev1","v1.2.0-dev2","v1.2.0-dev3","v1.2.0-dev4","v1.2.0-dev5"],"type":"string"},"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"hints":{"description":"Declares requirements that apply to either the runtime environment or the\nworkflow engine that must be met in order to execute this process.  If\nan implementation cannot satisfy all requirements, or a requirement is\nlisted which is not recognized by the implementation, it is a fatal\nerror and the implementation must not attempt to run the process,\nunless overridden at user option.","oneOf":[{"items":{"anyOf":[{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"},{"$ref":"#/definitions/InlineJavascriptRequirement"},{"$ref":"#/definitions/SchemaDefRequirement"},{"$ref":"#/definitions/LoadListingRequirement"},{"$ref":"#/definitions/DockerRequirement"},{"$ref":"#/definitions/SoftwareRequirement"},{"$ref":"#/definitions/InitialWorkDirRequirement"},{"$ref":"#/definitions/EnvVarRequirement"},{"$ref":"#/definitions/ShellCommandRequirement"},{"$ref":"#/definitions/ResourceRequirement"},{"$ref":"#/definitions/WorkReuse"},{"$ref":"#/definitions/NetworkAccess"},{"$ref":"#/definitions/InplaceUpdateRequirement"},{"$ref":"#/definitions/ToolTimeLimit"},{"$ref":"#/definitions/SubworkflowFeatureRequirement"},{"$ref":"#/definitions/ScatterFeatureRequirement"},{"$ref":"#/definitions/MultipleInputFeatureRequirement"},{"$ref":"#/definitions/StepInputExpressionRequirement"}]},"type":"array"},{"type":"object","properties":{"InlineJavascriptRequirement":{"anyOf":[{"$ref":"#/definitions/InlineJavascriptRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SchemaDefRequirement":{"anyOf":[{"$ref":"#/definitions/SchemaDefRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"LoadListingRequirement":{"anyOf":[{"$ref":"#/definitions/LoadListingRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"DockerRequirement":{"anyOf":[{"$ref":"#/definitions/DockerRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SoftwareRequirement":{"anyOf":[{"$ref":"#/definitions/SoftwareRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"InitialWorkDirRequirement":{"anyOf":[{"$ref":"#/definitions/InitialWorkDirRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"EnvVarRequirement":{"anyOf":[{"$ref":"#/definitions/EnvVarRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ShellCommandRequirement":{"anyOf":[{"$ref":"#/definitions/ShellCommandRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ResourceRequirement":{"anyOf":[{"$ref":"#/definitions/ResourceRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"WorkReuse":{"anyOf":[{"$ref":"#/definitions/WorkReuseMap"},{"type":"object","properties":{},"additionalProperties":false}]},"NetworkAccess":{"anyOf":[{"$ref":"#/definitions/NetworkAccessMap"},{"type":"object","properties":{},"additionalProperties":false}]},"InplaceUpdateRequirement":{"anyOf":[{"$ref":"#/definitions/InplaceUpdateRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ToolTimeLimit":{"anyOf":[{"$ref":"#/definitions/ToolTimeLimitMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SubworkflowFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/SubworkflowFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ScatterFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/ScatterFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"MultipleInputFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/MultipleInputFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"StepInputExpressionRequirement":{"anyOf":[{"$ref":"#/definitions/StepInputExpressionRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]}},"additionalProperties":false}]},"id":{"description":"The unique identifier for this object.\n\nOnly useful for `$graph` at `Process` level. Should not be exposed\nto users in graphical or terminal user interfaces.","type":"string"},"inputs":{"description":"Defines the input parameters of the process.  The process is ready to\nrun when all required input parameters are associated with concrete\nvalues.  Input parameters include a schema for each parameter which is\nused to validate the input object.  It may also be used to build a user\ninterface for constructing the input object.\n\nWhen accepting an input object, all input parameters must have a value.\nIf an input parameter is missing from the input object, it must be\nassigned a value of `null` (or the value of `default` for that\nparameter, if provided) for the purposes of validation and evaluation\nof expressions.","oneOf":[{"items":{"$ref":"#/definitions/OperationInputParameter"},"type":"array"},{"patternProperties":{"^[_a-zA-Z][a-zA-Z0-9_-]*$":{"oneOf":[{"$ref":"#/definitions/OperationInputParameter"},{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Specify valid types of data that may be assigned to this parameter."},{"type":"array","items":{"oneOf":[{"type":"string"},{"$ref":"#/definitions/OperationInputParameter"}]}}]}},"type":"object"}]},"intent":{"description":"An identifier for the type of computational operation, of this Process.\nEspecially useful for [`Operation`](Workflow.html#Operation), but can also be used for\n[`CommandLineTool`](CommandLineTool.html#CommandLineTool),\n[`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool).\n\nIf provided, then this must be an IRI of a concept node that\nrepresents the type of operation, preferably defined within an ontology.\n\nFor example, in the domain of bioinformatics, one can use an IRI from\nthe EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004),\nlike [Alignment](http://edamontology.org/operation_2928),\nor [Clustering](http://edamontology.org/operation_3432); or a more\nspecific Operation concept like\n[Split read mapping](http://edamontology.org/operation_3199).","items":{"type":"string"},"type":"array"},"label":{"description":"A short, human-readable label of this object.","type":"string"},"outputs":{"description":"Defines the parameters representing the output of the process.  May be\nused to generate and/or validate the output object.","oneOf":[{"items":{"$ref":"#/definitions/OperationOutputParameter"},"type":"array"},{"patternProperties":{"^[_a-zA-Z][a-zA-Z0-9_-]*$":{"oneOf":[{"$ref":"#/definitions/OperationOutputParameter"},{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Specify valid types of data that may be assigned to this parameter."},{"type":"array","items":{"oneOf":[{"type":"string"},{"$ref":"#/definitions/OperationOutputParameter"}]}}]}},"type":"object"}]},"requirements":{"description":"Declares requirements that apply to either the runtime environment or the\nworkflow engine that must be met in order to execute this process.  If\nan implementation cannot satisfy all requirements, or a requirement is\nlisted which is not recognized by the implementation, it is a fatal\nerror and the implementation must not attempt to run the process,\nunless overridden at user option.","oneOf":[{"items":{"anyOf":[{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"},{"$ref":"#/definitions/InlineJavascriptRequirement"},{"$ref":"#/definitions/SchemaDefRequirement"},{"$ref":"#/definitions/LoadListingRequirement"},{"$ref":"#/definitions/DockerRequirement"},{"$ref":"#/definitions/SoftwareRequirement"},{"$ref":"#/definitions/InitialWorkDirRequirement"},{"$ref":"#/definitions/EnvVarRequirement"},{"$ref":"#/definitions/ShellCommandRequirement"},{"$ref":"#/definitions/ResourceRequirement"},{"$ref":"#/definitions/WorkReuse"},{"$ref":"#/definitions/NetworkAccess"},{"$ref":"#/definitions/InplaceUpdateRequirement"},{"$ref":"#/definitions/ToolTimeLimit"},{"$ref":"#/definitions/SubworkflowFeatureRequirement"},{"$ref":"#/definitions/ScatterFeatureRequirement"},{"$ref":"#/definitions/MultipleInputFeatureRequirement"},{"$ref":"#/definitions/StepInputExpressionRequirement"}]},"type":"array"},{"type":"object","properties":{"InlineJavascriptRequirement":{"anyOf":[{"$ref":"#/definitions/InlineJavascriptRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SchemaDefRequirement":{"anyOf":[{"$ref":"#/definitions/SchemaDefRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"LoadListingRequirement":{"anyOf":[{"$ref":"#/definitions/LoadListingRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"DockerRequirement":{"anyOf":[{"$ref":"#/definitions/DockerRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SoftwareRequirement":{"anyOf":[{"$ref":"#/definitions/SoftwareRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"InitialWorkDirRequirement":{"anyOf":[{"$ref":"#/definitions/InitialWorkDirRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"EnvVarRequirement":{"anyOf":[{"$ref":"#/definitions/EnvVarRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ShellCommandRequirement":{"anyOf":[{"$ref":"#/definitions/ShellCommandRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ResourceRequirement":{"anyOf":[{"$ref":"#/definitions/ResourceRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"WorkReuse":{"anyOf":[{"$ref":"#/definitions/WorkReuseMap"},{"type":"object","properties":{},"additionalProperties":false}]},"NetworkAccess":{"anyOf":[{"$ref":"#/definitions/NetworkAccessMap"},{"type":"object","properties":{},"additionalProperties":false}]},"InplaceUpdateRequirement":{"anyOf":[{"$ref":"#/definitions/InplaceUpdateRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ToolTimeLimit":{"anyOf":[{"$ref":"#/definitions/ToolTimeLimitMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SubworkflowFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/SubworkflowFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ScatterFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/ScatterFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"MultipleInputFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/MultipleInputFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"StepInputExpressionRequirement":{"anyOf":[{"$ref":"#/definitions/StepInputExpressionRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]}},"additionalProperties":false}]}},"required":["class","inputs","outputs"],"type":"object"},"OperationInputParameter":{"additionalProperties":false,"description":"Describe an input parameter of an operation.","properties":{"default":{"description":"The default value to use for this parameter if the parameter is missing\nfrom the input object, or if the value of the parameter in the input\nobject is `null`.  Default values are applied before evaluating expressions\n(e.g. dependent `valueFrom` fields)."},"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"format":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nThis must be one or more IRIs of concept nodes\nthat represents file formats which are allowed as input to this\nparameter, preferably defined within an ontology.  If no ontology is\navailable, file formats may be tested by exact match."},"id":{"description":"The unique identifier for this object.","type":"string"},"label":{"description":"A short, human-readable label of this object.","type":"string"},"loadContents":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nIf true, the file (or each file in the array) must be a UTF-8\ntext file 64 KiB or smaller, and the implementation must read\nthe entire contents of the file (or file array) and place it\nin the `contents` field of the File object for use by\nexpressions.  If the size of the file is greater than 64 KiB,\nthe implementation must raise a fatal error.","type":"boolean"},"loadListing":{"description":"Only valid when `type: Directory` or is an array of `items: Directory`.\n\nSpecify the desired behavior for loading the `listing` field of\na Directory object for use by expressions.\n\nThe order of precedence for loadListing is:\n\n  1. `loadListing` on an individual parameter\n  2. Inherited from `LoadListingRequirement`\n  3. By default: `no_listing`","enum":["deep_listing","no_listing","shallow_listing"],"type":"string"},"secondaryFiles":{"anyOf":[{"$ref":"#/definitions/SecondaryFileSchema"},{"items":{"$ref":"#/definitions/SecondaryFileSchema"},"type":"array"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nProvides a pattern or expression specifying files or\ndirectories that should be included alongside the primary\nfile.  Secondary files may be required or optional.  When not\nexplicitly specified, secondary files specified for `inputs`\nare required and `outputs` are optional.  An implementation\nmust include matching Files and Directories in the\n`secondaryFiles` property of the primary file.  These Files\nand Directories must be transferred and staged alongside the\nprimary file.  An implementation may fail workflow execution\nif a required secondary file does not exist.\n\nIf the value is an expression, the value of `self` in the expression\nmust be the primary input or output File object to which this binding\napplies.  The `basename`, `nameroot` and `nameext` fields must be\npresent in `self`.  For `CommandLineTool` outputs the `path` field must\nalso be present.  The expression must return a filename string relative\nto the path to the primary File, a File or Directory object with either\n`path` or `location` and `basename` fields set, or an array consisting\nof strings or File or Directory objects.  It is legal to reference an\nunchanged File or Directory object taken from input as a secondaryFile.\nThe expression may return \"null\" in which case there is no secondaryFile\nfrom that expression.\n\nTo work on non-filename-preserving storage systems, portable tool\ndescriptions should avoid constructing new values from `location`, but\nshould construct relative references using `basename` or `nameroot`\ninstead.\n\nIf a value in `secondaryFiles` is a string that is not an expression,\nit specifies that the following pattern should be applied to the path\nof the primary file to yield a filename relative to the primary File:\n\n  1. If string ends with `?` character, remove the last `?` and mark\n    the resulting secondary file as optional.\n  2. If string begins with one or more caret `^` characters, for each\n    caret, remove the last file extension from the path (the last\n    period `.` and all following characters).  If there are no file\n    extensions, the path is unchanged.\n  3. Append the remainder of the string to the end of the file path."},"streamable":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nA value of `true` indicates that the file is read or written\nsequentially without seeking.  An implementation may use this flag to\nindicate whether it is valid to stream file contents using a named\npipe.  Default: `false`.","type":"boolean"},"type":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Specify valid types of data that may be assigned to this parameter."}},"required":["type"],"type":"object"},"OperationOutputParameter":{"additionalProperties":false,"description":"Describe an output parameter of an operation.","properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"format":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nThis is the file format that will be assigned to the output\nFile object.","type":"string"},"id":{"description":"The unique identifier for this object.","type":"string"},"label":{"description":"A short, human-readable label of this object.","type":"string"},"secondaryFiles":{"anyOf":[{"$ref":"#/definitions/SecondaryFileSchema"},{"items":{"$ref":"#/definitions/SecondaryFileSchema"},"type":"array"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nProvides a pattern or expression specifying files or\ndirectories that should be included alongside the primary\nfile.  Secondary files may be required or optional.  When not\nexplicitly specified, secondary files specified for `inputs`\nare required and `outputs` are optional.  An implementation\nmust include matching Files and Directories in the\n`secondaryFiles` property of the primary file.  These Files\nand Directories must be transferred and staged alongside the\nprimary file.  An implementation may fail workflow execution\nif a required secondary file does not exist.\n\nIf the value is an expression, the value of `self` in the expression\nmust be the primary input or output File object to which this binding\napplies.  The `basename`, `nameroot` and `nameext` fields must be\npresent in `self`.  For `CommandLineTool` outputs the `path` field must\nalso be present.  The expression must return a filename string relative\nto the path to the primary File, a File or Directory object with either\n`path` or `location` and `basename` fields set, or an array consisting\nof strings or File or Directory objects.  It is legal to reference an\nunchanged File or Directory object taken from input as a secondaryFile.\nThe expression may return \"null\" in which case there is no secondaryFile\nfrom that expression.\n\nTo work on non-filename-preserving storage systems, portable tool\ndescriptions should avoid constructing new values from `location`, but\nshould construct relative references using `basename` or `nameroot`\ninstead.\n\nIf a value in `secondaryFiles` is a string that is not an expression,\nit specifies that the following pattern should be applied to the path\nof the primary file to yield a filename relative to the primary File:\n\n  1. If string ends with `?` character, remove the last `?` and mark\n    the resulting secondary file as optional.\n  2. If string begins with one or more caret `^` characters, for each\n    caret, remove the last file extension from the path (the last\n    period `.` and all following characters).  If there are no file\n    extensions, the path is unchanged.\n  3. Append the remainder of the string to the end of the file path."},"streamable":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nA value of `true` indicates that the file is read or written\nsequentially without seeking.  An implementation may use this flag to\nindicate whether it is valid to stream file contents using a named\npipe.  Default: `false`.","type":"boolean"},"type":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Specify valid types of data that may be assigned to this parameter."}},"required":["type"],"type":"object"},"OutputArraySchema":{"additionalProperties":false,"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputArraySchema","properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"items":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Defines the type of the array elements."},"label":{"description":"A short, human-readable label of this object.","type":"string"},"name":{"description":"The identifier for this type","type":"string"},"type":{"const":"array","description":"Must be `array`","type":"string"}},"required":["items","type"],"type":"object"},"OutputEnumSchema":{"additionalProperties":false,"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputEnumSchema","properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"label":{"description":"A short, human-readable label of this object.","type":"string"},"name":{"description":"The identifier for this type","type":"string"},"symbols":{"description":"Defines the set of valid symbols.","items":{"type":"string"},"type":"array"},"type":{"const":"enum","description":"Must be `enum`","type":"string"}},"required":["symbols","type"],"type":"object"},"OutputRecordField":{"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordField","oneOf":[{"additionalProperties":false,"properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"format":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nThis is the file format that will be assigned to the output\nFile object.","type":"string"},"label":{"description":"A short, human-readable label of this object.","type":"string"},"name":{"description":"The name of the field","type":"string"},"secondaryFiles":{"anyOf":[{"$ref":"#/definitions/SecondaryFileSchema"},{"items":{"$ref":"#/definitions/SecondaryFileSchema"},"type":"array"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nProvides a pattern or expression specifying files or\ndirectories that should be included alongside the primary\nfile.  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The expression must return a filename string relative\nto the path to the primary File, a File or Directory object with either\n`path` or `location` and `basename` fields set, or an array consisting\nof strings or File or Directory objects.  It is legal to reference an\nunchanged File or Directory object taken from input as a secondaryFile.\nThe expression may return \"null\" in which case there is no secondaryFile\nfrom that expression.\n\nTo work on non-filename-preserving storage systems, portable tool\ndescriptions should avoid constructing new values from `location`, but\nshould construct relative references using `basename` or `nameroot`\ninstead.\n\nIf a value in `secondaryFiles` is a string that is not an expression,\nit specifies that the following pattern should be applied to the path\nof the primary file to yield a filename relative to the primary File:\n\n  1. If string ends with `?` character, remove the last `?` and mark\n    the resulting secondary file as optional.\n  2. If string begins with one or more caret `^` characters, for each\n    caret, remove the last file extension from the path (the last\n    period `.` and all following characters).  If there are no file\n    extensions, the path is unchanged.\n  3. Append the remainder of the string to the end of the file path."},"streamable":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nA value of `true` indicates that the file is read or written\nsequentially without seeking.  An implementation may use this flag to\nindicate whether it is valid to stream file contents using a named\npipe.  Default: `false`.","type":"boolean"},"type":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"The field type"}},"required":["name","type"],"type":"object"},{"type":"array","items":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"The field type"}}]},"OutputRecordSchema":{"additionalProperties":false,"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordSchema","properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"fields":{"description":"Defines the fields of the record.","oneOf":[{"items":{"$ref":"#/definitions/OutputRecordField"},"type":"array"},{"patternProperties":{"^[_a-zA-Z][a-zA-Z0-9_-]*$":{"$ref":"#/definitions/OutputRecordFieldMap"}},"type":"object"}]},"label":{"description":"A short, human-readable label of this object.","type":"string"},"name":{"description":"The identifier for this type","type":"string"},"type":{"const":"record","description":"Must be `record`","type":"string"}},"required":["type"],"type":"object"},"ResourceRequirement":{"additionalProperties":false,"description":"Specify basic hardware resource requirements.\n\n\"min\" is the minimum amount of a resource that must be reserved to\nschedule a job. If \"min\" cannot be satisfied, the job should not\nbe run.\n\n\"max\" is the maximum amount of a resource that the job shall be\nallocated. If a node has sufficient resources, multiple jobs may\nbe scheduled on a single node provided each job's \"max\" resource\nrequirements are met. If a job attempts to exceed its resource\nallocation, an implementation may deny additional resources, which\nmay result in job failure.\n\nIf both \"min\" and \"max\" are specified, an implementation may\nchoose to allocate any amount between \"min\" and \"max\", with the\nactual allocation provided in the `runtime` object.\n\nIf \"min\" is specified but \"max\" is not, then \"max\" == \"min\"\nIf \"max\" is specified by \"min\" is not, then \"min\" == \"max\".\n\nIt is an error if max < min.\n\nIt is an error if the value of any of these fields is negative.\n\nIf neither \"min\" nor \"max\" is specified for a resource, use the default values below.","properties":{"class":{"const":"ResourceRequirement","description":"Always 'ResourceRequirement'","type":"string"},"coresMax":{"description":"Maximum reserved number of CPU cores.\n\nSee `coresMin` for discussion about fractional CPU requests.","type":["string","number"]},"coresMin":{"description":"Minimum reserved number of CPU cores (default is 1).\n\nMay be a fractional value to indicate to a scheduling\nalgorithm that one core can be allocated to multiple\njobs. For example, a value of 0.25 indicates that up to 4\njobs may run in parallel on 1 core.  A value of 1.25 means\nthat up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\n\nProcesses can only share a core allocation if the sum of each\nof their `ramMax`, `tmpdirMax`, and `outdirMax` requests also\ndo not exceed the capacity of the node.\n\nProcesses sharing a core must have the same level of isolation\n(typically a container or VM) that they would normally have.\n\nThe reported number of CPU cores reserved for the process,\nwhich is available to expressions on the CommandLineTool as\n`runtime.cores`, must be a non-zero integer, and may be\ncalculated by rounding up the cores request to the next whole\nnumber.\n\nScheduling systems may allocate fractional CPU resources by\nsetting quotas or scheduling weights.  Scheduling systems that\ndo not support fractional CPUs may round up the request to the\nnext whole number.","type":["string","number"]},"outdirMax":{"description":"Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)\n\nSee `outdirMin` for discussion about fractional storage requests.","type":["string","number"]},"outdirMin":{"description":"Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) (default is 1024)\n\nMay be a fractional value.  If so, the actual storage request\nmust be rounded up to the next whole number.  The reported\namount of storage reserved for the process, which is available\nto expressions on the CommandLineTool as `runtime.outdirSize`,\nmust be a non-zero integer.","type":["string","number"]},"ramMax":{"description":"Maximum reserved RAM in mebibytes (2**20)\n\nSee `ramMin` for discussion about fractional RAM requests.","type":["string","number"]},"ramMin":{"description":"Minimum reserved RAM in mebibytes (2**20) (default is 256)\n\nMay be a fractional value.  If so, the actual RAM request must\nbe rounded up to the next whole number.  The reported amount of\nRAM reserved for the process, which is available to\nexpressions on the CommandLineTool as `runtime.ram`, must be a\nnon-zero integer.","type":["string","number"]},"tmpdirMax":{"description":"Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)\n\nSee `tmpdirMin` for discussion about fractional storage requests.","type":["string","number"]},"tmpdirMin":{"description":"Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) (default is 1024)\n\nMay be a fractional value.  If so, the actual storage request\nmust be rounded up to the next whole number.  The reported\namount of storage reserved for the process, which is available\nto expressions on the CommandLineTool as `runtime.tmpdirSize`,\nmust be a non-zero integer.","type":["string","number"]}},"required":["class"],"type":"object"},"ScatterFeatureRequirement":{"additionalProperties":false,"description":"Indicates that the workflow platform must support the `scatter` and\n`scatterMethod` fields of [WorkflowStep](#WorkflowStep).","properties":{"class":{"const":"ScatterFeatureRequirement","description":"Always 'ScatterFeatureRequirement'","type":"string"}},"required":["class"],"type":"object"},"SchemaDefRequirement":{"additionalProperties":false,"description":"This field consists of an array of type definitions which must be used when\ninterpreting the `inputs` and `outputs` fields.  When a `type` field\ncontains a IRI, the implementation must check if the type is defined in\n`schemaDefs` and use that definition.  If the type is not found in\n`schemaDefs`, it is an error.  The entries in `schemaDefs` must be\nprocessed in the order listed such that later schema definitions may refer\nto earlier schema definitions.\n\n- **Type definitions are allowed for `enum` and `record` types only.**\n- Type definitions may be shared by defining them in a file and then\n  `$include`-ing them in the `types` field.\n- A file can contain a list of type definitions","properties":{"class":{"const":"SchemaDefRequirement","description":"Always 'SchemaDefRequirement'","type":"string"},"types":{"description":"The list of type definitions.","items":{"anyOf":[{"anyOf":[{"$ref":"#/definitions/CommandInputArraySchema"},{"$ref":"#/definitions/CommandInputRecordSchema"},{"$ref":"#/definitions/CommandInputEnumSchema"}]},{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"}]},"type":"array"}},"required":["class","types"],"type":"object"},"SecondaryFileSchema":{"description":"Secondary files are specified using the following micro-DSL for secondary files:\n\n* If the value is a string, it is transformed to an object with two fields\n  `pattern` and `required`\n* By default, the value of `required` is `null`\n  (this indicates default behavior, which may be based on the context)\n* If the value ends with a question mark `?` the question mark is\n  stripped off and the value of the field `required` is set to `False`\n* The remaining value is assigned to the field `pattern`\n\nFor implementation details and examples, please see\n[this section](SchemaSalad.html#Domain_Specific_Language_for_secondary_files)\nin the Schema Salad specification.","oneOf":[{"additionalProperties":false,"properties":{"pattern":{"description":"Provides a pattern or expression specifying files or directories that\nshould be included alongside the primary file.\n\nIf the value is an expression, the value of `self` in the\nexpression must be the primary input or output File object to\nwhich this binding applies.  The `basename`, `nameroot` and\n`nameext` fields must be present in `self`.  For\n`CommandLineTool` inputs the `location` field must also be\npresent.  For `CommandLineTool` outputs the `path` field must\nalso be present.  If secondary files were included on an input\nFile object as part of the Process invocation, they must also\nbe present in `secondaryFiles` on `self`.\n\nThe expression must return either: a filename string relative\nto the path to the primary File, a File or Directory object\n(`class: File` or `class: Directory`) with either `location`\n(for inputs) or `path` (for outputs) and `basename` fields\nset, or an array consisting of strings or File or Directory\nobjects as previously described.\n\nIt is legal to use `location` from a File or Directory object\npassed in as input, including `location` from secondary files\non `self`.  If an expression returns a File object with the\nsame `location` but a different `basename` as a secondary file\nthat was passed in, the expression result takes precedence.\nSetting the basename with an expression this way affects the\n`path` where the secondary file will be staged to in the\nCommandLineTool.\n\nThe expression may return \"null\" in which case there is no\nsecondary file from that expression.\n\nTo work on non-filename-preserving storage systems, portable\ntool descriptions should treat `location` as an\n[opaque identifier](#opaque-strings) and avoid constructing new\nvalues from `location`, but should construct relative references\nusing `basename` or `nameroot` instead, or propagate `location`\nfrom defined inputs.\n\nIf a value in `secondaryFiles` is a string that is not an expression,\nit specifies that the following pattern should be applied to the path\nof the primary file to yield a filename relative to the primary File:\n\n  1. If string ends with `?` character, remove the last `?` and mark\n    the resulting secondary file as optional.\n  2. If string begins with one or more caret `^` characters, for each\n    caret, remove the last file extension from the path (the last\n    period `.` and all following characters).  If there are no file\n    extensions, the path is unchanged.\n  3. Append the remainder of the string to the end of the file path.","type":"string"},"required":{"description":"An implementation must not fail workflow execution if `required` is\nset to `false` and the expected secondary file does not exist.\nDefault value for `required` field is `true` for secondary files on\ninput and `false` for secondary files on output.","type":["string","boolean"]}},"required":["pattern"],"type":"object"},{"type":"string"}]},"ShellCommandRequirement":{"additionalProperties":false,"description":"Modify the behavior of CommandLineTool to generate a single string\ncontaining a shell command line.  Each item in the `arguments` list must\nbe joined into a string separated by single spaces and quoted to prevent\ninterpretation by the shell, unless `CommandLineBinding` for that argument\ncontains `shellQuote: false`.  If `shellQuote: false` is specified, the\nargument is joined into the command string without quoting, which allows\nthe use of shell metacharacters such as `|` for pipes.","properties":{"class":{"const":"ShellCommandRequirement","description":"Always 'ShellCommandRequirement'","type":"string"}},"required":["class"],"type":"object"},"SoftwarePackage":{"additionalProperties":false,"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#SoftwarePackage","properties":{"package":{"description":"The name of the software to be made available. If the name is\ncommon, inconsistent, or otherwise ambiguous it should be combined with\none or more identifiers in the `specs` field.","type":"string"},"specs":{"description":"One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s\nidentifying resources for installing or enabling the software named in\nthe `package` field. Implementations may provide resolvers which map\nthese software identifier IRIs to some configuration action; or they can\nuse only the name from the `package` field on a best effort basis.\n\nFor example, the IRI https://packages.debian.org/bowtie could\nbe resolved with `apt-get install bowtie`. The IRI\nhttps://anaconda.org/bioconda/bowtie could be resolved with `conda\ninstall -c bioconda bowtie`.\n\nIRIs can also be system independent and used to map to a specific\nsoftware installation or selection mechanism.\nUsing [RRID](https://www.identifiers.org/rrid/) as an example:\nhttps://identifiers.org/rrid/RRID:SCR_005476\ncould be fulfilled using the above-mentioned Debian or bioconda\npackage, a local installation managed by [Environment Modules](https://modules.sourceforge.net/),\nor any other mechanism the platform chooses. IRIs can also be from\nidentifier sources that are discipline specific yet still system\nindependent. As an example, the equivalent [ELIXIR Tools and Data\nService Registry](https://bio.tools) IRI to the previous RRID example is\nhttps://bio.tools/tool/bowtie2/version/2.2.8.\nIf supported by a given registry, implementations are encouraged to\nquery these system independent software identifier IRIs directly for\nlinks to packaging systems.\n\nA site specific IRI can be listed as well. For example, an academic\ncomputing cluster using Environment Modules could list the IRI\n`https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that\n`module load bowtie-tbb/1.1.2` should be executed to make available\n`bowtie` version 1.1.2 compiled with the TBB library prior to running\nthe accompanying Workflow or CommandLineTool. Note that the example IRI\nis specific to a particular institution and computing environment as\nthe Environment Modules system does not have a common namespace or\nstandardized naming convention.\n\nThis last example is the least portable and should only be used if\nmechanisms based off of the `package` field or more generic IRIs are\nunavailable or unsuitable. While harmless to other sites, site specific\nsoftware IRIs should be left out of shared CWL descriptions to avoid\nclutter.","items":{"type":"string"},"type":"array"},"version":{"description":"The (optional) versions of the software that are known to be\ncompatible.","items":{"type":"string"},"type":"array"}},"required":["package"],"type":"object"},"SoftwareRequirement":{"additionalProperties":false,"description":"A list of software packages that should be configured in the environment of\nthe defined process.","properties":{"class":{"const":"SoftwareRequirement","description":"Always 'SoftwareRequirement'","type":"string"},"packages":{"description":"The list of software to be configured.","items":{"anyOf":[{"$ref":"#/definitions/SoftwarePackage"},{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"}]},"type":"array"}},"required":["class","packages"],"type":"object"},"StepInputExpressionRequirement":{"additionalProperties":false,"description":"Indicate that the workflow platform must support the `valueFrom` field\nof [WorkflowStepInput](#WorkflowStepInput).","properties":{"class":{"const":"StepInputExpressionRequirement","description":"Always 'StepInputExpressionRequirement'","type":"string"}},"required":["class"],"type":"object"},"SubworkflowFeatureRequirement":{"additionalProperties":false,"description":"Indicates that the workflow platform must support nested workflows in\nthe `run` field of [WorkflowStep](#WorkflowStep).","properties":{"class":{"const":"SubworkflowFeatureRequirement","description":"Always 'SubworkflowFeatureRequirement'","type":"string"}},"required":["class"],"type":"object"},"T":{"additionalProperties":false,"type":"object"},"ToolTimeLimit":{"additionalProperties":false,"description":"Set an upper limit on the execution time of a CommandLineTool.\nA CommandLineTool whose execution duration exceeds the time\nlimit may be preemptively terminated and considered failed.\nMay also be used by batch systems to make scheduling decisions.\nThe execution duration excludes external operations, such as\nstaging of files, pulling a docker image etc, and only counts\nwall-time for the execution of the command line itself.","properties":{"class":{"const":"ToolTimeLimit","description":"Always 'ToolTimeLimit'","type":"string"},"timelimit":{"description":"The time limit, in seconds.  A time limit of zero means no\ntime limit.  Negative time limits are an error.","type":["string","number"]}},"required":["class","timelimit"],"type":"object"},"WorkReuse":{"additionalProperties":false,"description":"For implementations that support reusing output from past work (on\nthe assumption that same code and same input produce same\nresults), control whether to enable or disable the reuse behavior\nfor a particular tool or step (to accommodate situations where that\nassumption is incorrect).  A reused step is not executed but\ninstead returns the same output as the original execution.\n\nIf `WorkReuse` is not specified, correct tools should assume it\nis enabled by default.","properties":{"class":{"const":"WorkReuse","description":"Always 'WorkReuse'","type":"string"},"enableReuse":{"type":["string","boolean"]}},"required":["class","enableReuse"],"type":"object"},"Workflow":{"description":"A workflow describes a set of **steps** and the **dependencies** between\nthose steps.  When a step produces output that will be consumed by a\nsecond step, the first step is a dependency of the second step.\n\nWhen there is a dependency, the workflow engine must execute the preceding\nstep and wait for it to successfully produce output before executing the\ndependent step.  If two steps are defined in the workflow graph that\nare not directly or indirectly dependent, these steps are **independent**,\nand may execute in any order or execute concurrently.  A workflow is\ncomplete when all steps have been executed.\n\nDependencies between parameters are expressed using the `source`\nfield on [workflow step input parameters](#WorkflowStepInput) and\n`outputSource` field on [workflow output\nparameters](#WorkflowOutputParameter).\n\nThe `source` field on each workflow step input parameter expresses\nthe data links that contribute to the value of the step input\nparameter (the \"sink\").  A workflow step can only begin execution\nwhen every data link connected to a step has been fulfilled.\n\nThe `outputSource` field on each workflow step input parameter\nexpresses the data links that contribute to the value of the\nworkflow output parameter (the \"sink\").  Workflow execution cannot\ncomplete successfully until every data link connected to an output\nparameter has been fulfilled.\n\n## Workflow success and failure\n\nA completed step must result in one of `success`, `temporaryFailure` or\n`permanentFailure` states.  An implementation may choose to retry a step\nexecution which resulted in `temporaryFailure`.  An implementation may\nchoose to either continue running other steps of a workflow, or terminate\nimmediately upon `permanentFailure`.\n\n* If any step of a workflow execution results in `permanentFailure`, then\nthe workflow status is `permanentFailure`.\n\n* If one or more steps result in `temporaryFailure` and all other steps\ncomplete `success` or are not executed, then the workflow status is\n`temporaryFailure`.\n\n* If all workflow steps are executed and complete with `success`, then the\nworkflow status is `success`.\n\n# Extensions\n\n[ScatterFeatureRequirement](#ScatterFeatureRequirement) and\n[SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) are\navailable as standard [extensions](#Extensions_and_Metadata) to core\nworkflow semantics.","properties":{"class":{"const":"Workflow","type":"string"},"cwlVersion":{"description":"CWL document version. Always required at the document root. Not\nrequired for a Process embedded inside another Process.","enum":["draft-2","draft-3","draft-3.dev1","draft-3.dev2","draft-3.dev3","draft-3.dev4","draft-3.dev5","draft-4.dev1","draft-4.dev2","draft-4.dev3","v1.0","v1.0.dev4","v1.1","v1.1.0-dev1","v1.2","v1.2.0-dev1","v1.2.0-dev2","v1.2.0-dev3","v1.2.0-dev4","v1.2.0-dev5"],"type":"string"},"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"hints":{"description":"Declares requirements that apply to either the runtime environment or the\nworkflow engine that must be met in order to execute this process.  If\nan implementation cannot satisfy all requirements, or a requirement is\nlisted which is not recognized by the implementation, it is a fatal\nerror and the implementation must not attempt to run the process,\nunless overridden at user option.","oneOf":[{"items":{"anyOf":[{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"},{"$ref":"#/definitions/InlineJavascriptRequirement"},{"$ref":"#/definitions/SchemaDefRequirement"},{"$ref":"#/definitions/LoadListingRequirement"},{"$ref":"#/definitions/DockerRequirement"},{"$ref":"#/definitions/SoftwareRequirement"},{"$ref":"#/definitions/InitialWorkDirRequirement"},{"$ref":"#/definitions/EnvVarRequirement"},{"$ref":"#/definitions/ShellCommandRequirement"},{"$ref":"#/definitions/ResourceRequirement"},{"$ref":"#/definitions/WorkReuse"},{"$ref":"#/definitions/NetworkAccess"},{"$ref":"#/definitions/InplaceUpdateRequirement"},{"$ref":"#/definitions/ToolTimeLimit"},{"$ref":"#/definitions/SubworkflowFeatureRequirement"},{"$ref":"#/definitions/ScatterFeatureRequirement"},{"$ref":"#/definitions/MultipleInputFeatureRequirement"},{"$ref":"#/definitions/StepInputExpressionRequirement"}]},"type":"array"},{"type":"object","properties":{"InlineJavascriptRequirement":{"anyOf":[{"$ref":"#/definitions/InlineJavascriptRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SchemaDefRequirement":{"anyOf":[{"$ref":"#/definitions/SchemaDefRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"LoadListingRequirement":{"anyOf":[{"$ref":"#/definitions/LoadListingRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"DockerRequirement":{"anyOf":[{"$ref":"#/definitions/DockerRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SoftwareRequirement":{"anyOf":[{"$ref":"#/definitions/SoftwareRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"InitialWorkDirRequirement":{"anyOf":[{"$ref":"#/definitions/InitialWorkDirRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"EnvVarRequirement":{"anyOf":[{"$ref":"#/definitions/EnvVarRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ShellCommandRequirement":{"anyOf":[{"$ref":"#/definitions/ShellCommandRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ResourceRequirement":{"anyOf":[{"$ref":"#/definitions/ResourceRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"WorkReuse":{"anyOf":[{"$ref":"#/definitions/WorkReuseMap"},{"type":"object","properties":{},"additionalProperties":false}]},"NetworkAccess":{"anyOf":[{"$ref":"#/definitions/NetworkAccessMap"},{"type":"object","properties":{},"additionalProperties":false}]},"InplaceUpdateRequirement":{"anyOf":[{"$ref":"#/definitions/InplaceUpdateRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ToolTimeLimit":{"anyOf":[{"$ref":"#/definitions/ToolTimeLimitMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SubworkflowFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/SubworkflowFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ScatterFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/ScatterFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"MultipleInputFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/MultipleInputFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"StepInputExpressionRequirement":{"anyOf":[{"$ref":"#/definitions/StepInputExpressionRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]}},"additionalProperties":false}]},"id":{"description":"The unique identifier for this object.\n\nOnly useful for `$graph` at `Process` level. Should not be exposed\nto users in graphical or terminal user interfaces.","type":"string"},"inputs":{"description":"Defines the input parameters of the process.  The process is ready to\nrun when all required input parameters are associated with concrete\nvalues.  Input parameters include a schema for each parameter which is\nused to validate the input object.  It may also be used to build a user\ninterface for constructing the input object.\n\nWhen accepting an input object, all input parameters must have a value.\nIf an input parameter is missing from the input object, it must be\nassigned a value of `null` (or the value of `default` for that\nparameter, if provided) for the purposes of validation and evaluation\nof expressions.","oneOf":[{"items":{"$ref":"#/definitions/WorkflowInputParameter"},"type":"array"},{"patternProperties":{"^[_a-zA-Z][a-zA-Z0-9_-]*$":{"oneOf":[{"$ref":"#/definitions/WorkflowInputParameter"},{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Specify valid types of data that may be assigned to this parameter."},{"type":"array","items":{"oneOf":[{"type":"string"},{"$ref":"#/definitions/WorkflowInputParameter"}]}}]}},"type":"object"}]},"intent":{"description":"An identifier for the type of computational operation, of this Process.\nEspecially useful for [`Operation`](Workflow.html#Operation), but can also be used for\n[`CommandLineTool`](CommandLineTool.html#CommandLineTool),\n[`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool).\n\nIf provided, then this must be an IRI of a concept node that\nrepresents the type of operation, preferably defined within an ontology.\n\nFor example, in the domain of bioinformatics, one can use an IRI from\nthe EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004),\nlike [Alignment](http://edamontology.org/operation_2928),\nor [Clustering](http://edamontology.org/operation_3432); or a more\nspecific Operation concept like\n[Split read mapping](http://edamontology.org/operation_3199).","items":{"type":"string"},"type":"array"},"label":{"description":"A short, human-readable label of this object.","type":"string"},"outputs":{"description":"Defines the parameters representing the output of the process.  May be\nused to generate and/or validate the output object.","oneOf":[{"items":{"$ref":"#/definitions/WorkflowOutputParameter"},"type":"array"},{"patternProperties":{"^[_a-zA-Z][a-zA-Z0-9_-]*$":{"oneOf":[{"$ref":"#/definitions/WorkflowOutputParameter"},{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Specify valid types of data that may be assigned to this parameter."},{"type":"array","items":{"oneOf":[{"type":"string"},{"$ref":"#/definitions/WorkflowOutputParameter"}]}}]}},"type":"object"}]},"requirements":{"description":"Declares requirements that apply to either the runtime environment or the\nworkflow engine that must be met in order to execute this process.  If\nan implementation cannot satisfy all requirements, or a requirement is\nlisted which is not recognized by the implementation, it is a fatal\nerror and the implementation must not attempt to run the process,\nunless overridden at user option.","oneOf":[{"items":{"anyOf":[{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"},{"$ref":"#/definitions/InlineJavascriptRequirement"},{"$ref":"#/definitions/SchemaDefRequirement"},{"$ref":"#/definitions/LoadListingRequirement"},{"$ref":"#/definitions/DockerRequirement"},{"$ref":"#/definitions/SoftwareRequirement"},{"$ref":"#/definitions/InitialWorkDirRequirement"},{"$ref":"#/definitions/EnvVarRequirement"},{"$ref":"#/definitions/ShellCommandRequirement"},{"$ref":"#/definitions/ResourceRequirement"},{"$ref":"#/definitions/WorkReuse"},{"$ref":"#/definitions/NetworkAccess"},{"$ref":"#/definitions/InplaceUpdateRequirement"},{"$ref":"#/definitions/ToolTimeLimit"},{"$ref":"#/definitions/SubworkflowFeatureRequirement"},{"$ref":"#/definitions/ScatterFeatureRequirement"},{"$ref":"#/definitions/MultipleInputFeatureRequirement"},{"$ref":"#/definitions/StepInputExpressionRequirement"}]},"type":"array"},{"type":"object","properties":{"InlineJavascriptRequirement":{"anyOf":[{"$ref":"#/definitions/InlineJavascriptRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SchemaDefRequirement":{"anyOf":[{"$ref":"#/definitions/SchemaDefRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"LoadListingRequirement":{"anyOf":[{"$ref":"#/definitions/LoadListingRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"DockerRequirement":{"anyOf":[{"$ref":"#/definitions/DockerRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SoftwareRequirement":{"anyOf":[{"$ref":"#/definitions/SoftwareRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"InitialWorkDirRequirement":{"anyOf":[{"$ref":"#/definitions/InitialWorkDirRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"EnvVarRequirement":{"anyOf":[{"$ref":"#/definitions/EnvVarRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ShellCommandRequirement":{"anyOf":[{"$ref":"#/definitions/ShellCommandRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ResourceRequirement":{"anyOf":[{"$ref":"#/definitions/ResourceRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"WorkReuse":{"anyOf":[{"$ref":"#/definitions/WorkReuseMap"},{"type":"object","properties":{},"additionalProperties":false}]},"NetworkAccess":{"anyOf":[{"$ref":"#/definitions/NetworkAccessMap"},{"type":"object","properties":{},"additionalProperties":false}]},"InplaceUpdateRequirement":{"anyOf":[{"$ref":"#/definitions/InplaceUpdateRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ToolTimeLimit":{"anyOf":[{"$ref":"#/definitions/ToolTimeLimitMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SubworkflowFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/SubworkflowFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ScatterFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/ScatterFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"MultipleInputFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/MultipleInputFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"StepInputExpressionRequirement":{"anyOf":[{"$ref":"#/definitions/StepInputExpressionRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]}},"additionalProperties":false}]},"steps":{"description":"The individual steps that make up the workflow.  Each step is executed when all of its\ninput data links are fulfilled.  An implementation may choose to execute\nthe steps in a different order than listed and/or execute steps\nconcurrently, provided that dependencies between steps are met.","oneOf":[{"items":{"$ref":"#/definitions/WorkflowStep"},"type":"array"},{"patternProperties":{"^[_a-zA-Z][a-zA-Z0-9_-]*$":{"$ref":"#/definitions/WorkflowStep"}},"type":"object"}]}},"required":["class","inputs","outputs","steps"],"type":"object"},"WorkflowInputParameter":{"additionalProperties":false,"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowInputParameter","properties":{"default":{"description":"The default value to use for this parameter if the parameter is missing\nfrom the input object, or if the value of the parameter in the input\nobject is `null`.  Default values are applied before evaluating expressions\n(e.g. dependent `valueFrom` fields)."},"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"format":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nThis must be one or more IRIs of concept nodes\nthat represents file formats which are allowed as input to this\nparameter, preferably defined within an ontology.  If no ontology is\navailable, file formats may be tested by exact match."},"id":{"description":"The unique identifier for this object.","type":"string"},"inputBinding":{"$ref":"#/definitions/InputBinding","description":"Deprecated.  Preserved for v1.0 backwards compatibility.  Will be removed in\nCWL v2.0.  Use `WorkflowInputParameter.loadContents` instead."},"label":{"description":"A short, human-readable label of this object.","type":"string"},"loadContents":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nIf true, the file (or each file in the array) must be a UTF-8\ntext file 64 KiB or smaller, and the implementation must read\nthe entire contents of the file (or file array) and place it\nin the `contents` field of the File object for use by\nexpressions.  If the size of the file is greater than 64 KiB,\nthe implementation must raise a fatal error.","type":"boolean"},"loadListing":{"description":"Only valid when `type: Directory` or is an array of `items: Directory`.\n\nSpecify the desired behavior for loading the `listing` field of\na Directory object for use by expressions.\n\nThe order of precedence for loadListing is:\n\n  1. `loadListing` on an individual parameter\n  2. Inherited from `LoadListingRequirement`\n  3. By default: `no_listing`","enum":["deep_listing","no_listing","shallow_listing"],"type":"string"},"secondaryFiles":{"anyOf":[{"$ref":"#/definitions/SecondaryFileSchema"},{"items":{"$ref":"#/definitions/SecondaryFileSchema"},"type":"array"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nProvides a pattern or expression specifying files or\ndirectories that should be included alongside the primary\nfile.  Secondary files may be required or optional.  When not\nexplicitly specified, secondary files specified for `inputs`\nare required and `outputs` are optional.  An implementation\nmust include matching Files and Directories in the\n`secondaryFiles` property of the primary file.  These Files\nand Directories must be transferred and staged alongside the\nprimary file.  An implementation may fail workflow execution\nif a required secondary file does not exist.\n\nIf the value is an expression, the value of `self` in the expression\nmust be the primary input or output File object to which this binding\napplies.  The `basename`, `nameroot` and `nameext` fields must be\npresent in `self`.  For `CommandLineTool` outputs the `path` field must\nalso be present.  The expression must return a filename string relative\nto the path to the primary File, a File or Directory object with either\n`path` or `location` and `basename` fields set, or an array consisting\nof strings or File or Directory objects.  It is legal to reference an\nunchanged File or Directory object taken from input as a secondaryFile.\nThe expression may return \"null\" in which case there is no secondaryFile\nfrom that expression.\n\nTo work on non-filename-preserving storage systems, portable tool\ndescriptions should avoid constructing new values from `location`, but\nshould construct relative references using `basename` or `nameroot`\ninstead.\n\nIf a value in `secondaryFiles` is a string that is not an expression,\nit specifies that the following pattern should be applied to the path\nof the primary file to yield a filename relative to the primary File:\n\n  1. If string ends with `?` character, remove the last `?` and mark\n    the resulting secondary file as optional.\n  2. If string begins with one or more caret `^` characters, for each\n    caret, remove the last file extension from the path (the last\n    period `.` and all following characters).  If there are no file\n    extensions, the path is unchanged.\n  3. Append the remainder of the string to the end of the file path."},"streamable":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nA value of `true` indicates that the file is read or written\nsequentially without seeking.  An implementation may use this flag to\nindicate whether it is valid to stream file contents using a named\npipe.  Default: `false`.","type":"boolean"},"type":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Specify valid types of data that may be assigned to this parameter."}},"required":["type"],"type":"object"},"WorkflowOutputParameter":{"additionalProperties":false,"description":"Describe an output parameter of a workflow.  The parameter must be\nconnected to one or more parameters defined in the workflow that\nwill provide the value of the output parameter. It is legal to\nconnect a WorkflowInputParameter to a WorkflowOutputParameter.\n\nSee [WorkflowStepInput](#WorkflowStepInput) for discussion of\n`linkMerge` and `pickValue`.","properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"format":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nThis is the file format that will be assigned to the output\nFile object.","type":"string"},"id":{"description":"The unique identifier for this object.","type":"string"},"label":{"description":"A short, human-readable label of this object.","type":"string"},"linkMerge":{"description":"The method to use to merge multiple sources into a single array.\nIf not specified, the default method is \"merge_nested\".","enum":["merge_flattened","merge_nested"],"type":"string"},"outputSource":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"Specifies one or more names of an output from a workflow step (in the form\n`step_name/output_name` with a `/` separator`), or a workflow input name,\nthat supply their value(s) to the output parameter.\nthe output parameter.  It is valid to reference workflow level inputs\nhere."},"pickValue":{"description":"The method to use to choose non-null elements among multiple sources.","enum":["all_non_null","first_non_null","the_only_non_null"],"type":"string"},"secondaryFiles":{"anyOf":[{"$ref":"#/definitions/SecondaryFileSchema"},{"items":{"$ref":"#/definitions/SecondaryFileSchema"},"type":"array"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nProvides a pattern or expression specifying files or\ndirectories that should be included alongside the primary\nfile.  Secondary files may be required or optional.  When not\nexplicitly specified, secondary files specified for `inputs`\nare required and `outputs` are optional.  An implementation\nmust include matching Files and Directories in the\n`secondaryFiles` property of the primary file.  These Files\nand Directories must be transferred and staged alongside the\nprimary file.  An implementation may fail workflow execution\nif a required secondary file does not exist.\n\nIf the value is an expression, the value of `self` in the expression\nmust be the primary input or output File object to which this binding\napplies.  The `basename`, `nameroot` and `nameext` fields must be\npresent in `self`.  For `CommandLineTool` outputs the `path` field must\nalso be present.  The expression must return a filename string relative\nto the path to the primary File, a File or Directory object with either\n`path` or `location` and `basename` fields set, or an array consisting\nof strings or File or Directory objects.  It is legal to reference an\nunchanged File or Directory object taken from input as a secondaryFile.\nThe expression may return \"null\" in which case there is no secondaryFile\nfrom that expression.\n\nTo work on non-filename-preserving storage systems, portable tool\ndescriptions should avoid constructing new values from `location`, but\nshould construct relative references using `basename` or `nameroot`\ninstead.\n\nIf a value in `secondaryFiles` is a string that is not an expression,\nit specifies that the following pattern should be applied to the path\nof the primary file to yield a filename relative to the primary File:\n\n  1. If string ends with `?` character, remove the last `?` and mark\n    the resulting secondary file as optional.\n  2. If string begins with one or more caret `^` characters, for each\n    caret, remove the last file extension from the path (the last\n    period `.` and all following characters).  If there are no file\n    extensions, the path is unchanged.\n  3. Append the remainder of the string to the end of the file path."},"streamable":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nA value of `true` indicates that the file is read or written\nsequentially without seeking.  An implementation may use this flag to\nindicate whether it is valid to stream file contents using a named\npipe.  Default: `false`.","type":"boolean"},"type":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"Specify valid types of data that may be assigned to this parameter."}},"required":["type"],"type":"object"},"WorkflowStep":{"additionalProperties":false,"description":"A workflow step is an executable element of a workflow.  It specifies the\nunderlying process implementation (such as `CommandLineTool` or another\n`Workflow`) in the `run` field and connects the input and output parameters\nof the underlying process to workflow parameters.\n\n# Scatter/gather\n\nTo use scatter/gather,\n[ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified\nin the workflow or workflow step requirements.\n\nA \"scatter\" operation specifies that the associated workflow step or\nsubworkflow should execute separately over a list of input elements.  Each\njob making up a scatter operation is independent and may be executed\nconcurrently.\n\nThe `scatter` field specifies one or more input parameters which will be\nscattered.  An input parameter may be listed more than once.  The declared\ntype of each input parameter implicitly becomes an array of items of the\ninput parameter type.  If a parameter is listed more than once, it becomes\na nested array.  As a result, upstream parameters which are connected to\nscattered parameters must be arrays.\n\nAll output parameter types are also implicitly wrapped in arrays.  Each job\nin the scatter results in an entry in the output array.\n\nIf any scattered parameter runtime value is an empty array, all outputs are\nset to empty arrays and no work is done for the step, according to\napplicable scattering rules.\n\nIf `scatter` declares more than one input parameter, `scatterMethod`\ndescribes how to decompose the input into a discrete set of jobs.\n\n  * **dotproduct** specifies that each of the input arrays are aligned and one\n      element taken from each array to construct each job.  It is an error\n      if all input arrays are not the same length.\n\n  * **nested_crossproduct** specifies the Cartesian product of the inputs,\n      producing a job for every combination of the scattered inputs.  The\n      output must be nested arrays for each level of scattering, in the\n      order that the input arrays are listed in the `scatter` field.\n\n  * **flat_crossproduct** specifies the Cartesian product of the inputs,\n      producing a job for every combination of the scattered inputs.  The\n      output arrays must be flattened to a single level, but otherwise listed in the\n      order that the input arrays are listed in the `scatter` field.\n\n# Conditional execution (Optional)\n\nConditional execution makes execution of a step conditional on an\nexpression.  A step that is not executed is \"skipped\".  A skipped\nstep produces `null` for all output parameters.\n\nThe condition is evaluated after `scatter`, using the input object\nof each individual scatter job.  This means over a set of scatter\njobs, some may be executed and some may be skipped.  When the\nresults are gathered, skipped steps must be `null` in the output\narrays.\n\nThe `when` field controls conditional execution.  This is an\nexpression that must be evaluated with `inputs` bound to the step\ninput object (or individual scatter job), and returns a boolean\nvalue.  It is an error if this expression returns a value other\nthan `true` or `false`.\n\nConditionals in CWL are an optional feature and are not required\nto be implemented by all consumers of CWL documents.  An\nimplementation that does not support conditionals must return a\nfatal error when attempting to execute a workflow that uses\nconditional constructs the implementation does not support.\n\n# Subworkflows\n\nTo specify a nested workflow as part of a workflow step,\n[SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) must be\nspecified in the workflow or workflow step requirements.\n\nIt is a fatal error if a workflow directly or indirectly invokes itself as\na subworkflow (recursive workflows are not allowed).","properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"hints":{"description":"Declares hints applying to either the runtime environment or the\nworkflow engine that may be helpful in executing this workflow step.  It is\nnot an error if an implementation cannot satisfy all hints, however\nthe implementation may report a warning.","items":{},"type":"array"},"id":{"description":"The unique identifier for this object.","type":"string"},"in":{"description":"Defines the input parameters of the workflow step.  The process is ready to\nrun when all required input parameters are associated with concrete\nvalues.  Input parameters include a schema for each parameter which is\nused to validate the input object.  It may also be used build a user\ninterface for constructing the input object.","oneOf":[{"items":{"$ref":"#/definitions/WorkflowStepInput"},"type":"array"},{"patternProperties":{"^[_a-zA-Z][a-zA-Z0-9_-]*$":{"oneOf":[{"$ref":"#/definitions/WorkflowStepInput"},{"type":"string"},{"type":"array","items":{"oneOf":[{"type":"string"},{"$ref":"#/definitions/WorkflowStepInput"}]}}]}},"type":"object"}]},"label":{"description":"A short, human-readable label of this object.","type":"string"},"out":{"description":"Defines the parameters representing the output of the process.  May be\nused to generate and/or validate the output object.","items":{"anyOf":[{"$ref":"#/definitions/WorkflowStepOutput"},{"type":"string"}]},"type":"array"},"requirements":{"description":"Declares requirements that apply to either the runtime environment or the\nworkflow engine that must be met in order to execute this workflow step.  If\nan implementation cannot satisfy all requirements, or a requirement is\nlisted which is not recognized by the implementation, it is a fatal\nerror and the implementation must not attempt to run the process,\nunless overridden at user option.","oneOf":[{"items":{"anyOf":[{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"},{"$ref":"#/definitions/InlineJavascriptRequirement"},{"$ref":"#/definitions/SchemaDefRequirement"},{"$ref":"#/definitions/LoadListingRequirement"},{"$ref":"#/definitions/DockerRequirement"},{"$ref":"#/definitions/SoftwareRequirement"},{"$ref":"#/definitions/InitialWorkDirRequirement"},{"$ref":"#/definitions/EnvVarRequirement"},{"$ref":"#/definitions/ShellCommandRequirement"},{"$ref":"#/definitions/ResourceRequirement"},{"$ref":"#/definitions/WorkReuse"},{"$ref":"#/definitions/NetworkAccess"},{"$ref":"#/definitions/InplaceUpdateRequirement"},{"$ref":"#/definitions/ToolTimeLimit"},{"$ref":"#/definitions/SubworkflowFeatureRequirement"},{"$ref":"#/definitions/ScatterFeatureRequirement"},{"$ref":"#/definitions/MultipleInputFeatureRequirement"},{"$ref":"#/definitions/StepInputExpressionRequirement"}]},"type":"array"},{"type":"object","properties":{"InlineJavascriptRequirement":{"anyOf":[{"$ref":"#/definitions/InlineJavascriptRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SchemaDefRequirement":{"anyOf":[{"$ref":"#/definitions/SchemaDefRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"LoadListingRequirement":{"anyOf":[{"$ref":"#/definitions/LoadListingRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"DockerRequirement":{"anyOf":[{"$ref":"#/definitions/DockerRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SoftwareRequirement":{"anyOf":[{"$ref":"#/definitions/SoftwareRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"InitialWorkDirRequirement":{"anyOf":[{"$ref":"#/definitions/InitialWorkDirRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"EnvVarRequirement":{"anyOf":[{"$ref":"#/definitions/EnvVarRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ShellCommandRequirement":{"anyOf":[{"$ref":"#/definitions/ShellCommandRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ResourceRequirement":{"anyOf":[{"$ref":"#/definitions/ResourceRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"WorkReuse":{"anyOf":[{"$ref":"#/definitions/WorkReuseMap"},{"type":"object","properties":{},"additionalProperties":false}]},"NetworkAccess":{"anyOf":[{"$ref":"#/definitions/NetworkAccessMap"},{"type":"object","properties":{},"additionalProperties":false}]},"InplaceUpdateRequirement":{"anyOf":[{"$ref":"#/definitions/InplaceUpdateRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ToolTimeLimit":{"anyOf":[{"$ref":"#/definitions/ToolTimeLimitMap"},{"type":"object","properties":{},"additionalProperties":false}]},"SubworkflowFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/SubworkflowFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"ScatterFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/ScatterFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"MultipleInputFeatureRequirement":{"anyOf":[{"$ref":"#/definitions/MultipleInputFeatureRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]},"StepInputExpressionRequirement":{"anyOf":[{"$ref":"#/definitions/StepInputExpressionRequirementMap"},{"type":"object","properties":{},"additionalProperties":false}]}},"additionalProperties":false}]},"run":{"anyOf":[{"$ref":"#/definitions/CommandLineTool"},{"$ref":"#/definitions/ExpressionTool"},{"$ref":"#/definitions/Workflow"},{"$ref":"#/definitions/Operation"},{"type":"string"}],"description":"Specifies the process to run.  If `run` is a string, it must be an absolute IRI\nor a relative path from the primary document."},"scatter":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}]},"scatterMethod":{"description":"Required if `scatter` is an array of more than one element.","enum":["dotproduct","flat_crossproduct","nested_crossproduct"],"type":"string"},"when":{"description":"If defined, only run the step when the expression evaluates to\n`true`.  If `false` the step is skipped.  A skipped step\nproduces a `null` on each output.","type":"string"}},"required":["in","out","run"],"type":"object"},"WorkflowStepInput":{"additionalProperties":false,"description":"The input of a workflow step connects an upstream parameter (from the\nworkflow inputs, or the outputs of other workflows steps) with the input\nparameters of the process specified by the `run` field. Only input parameters\ndeclared by the target process will be passed through at runtime to the process\nthough additional parameters may be specified (for use within `valueFrom`\nexpressions for instance) - unconnected or unused parameters do not represent an\nerror condition.\n\n# Input object\n\nA WorkflowStepInput object must contain an `id` field in the form\n`#fieldname` or `#prefix/fieldname`.  When the `id` field contains a slash\n`/` the field name consists of the characters following the final slash\n(the prefix portion may contain one or more slashes to indicate scope).\nThis defines a field of the workflow step input object with the value of\nthe `source` parameter(s).\n\n# Merging multiple inbound data links\n\nTo merge multiple inbound data links,\n[MultipleInputFeatureRequirement](#MultipleInputFeatureRequirement) must be specified\nin the workflow or workflow step requirements.\n\nIf the sink parameter is an array, or named in a [workflow\nscatter](#WorkflowStep) operation, there may be multiple inbound\ndata links listed in the `source` field.  The values from the\ninput links are merged depending on the method specified in the\n`linkMerge` field.  If both `linkMerge` and `pickValue` are null\nor not specified, and there is more than one element in the\n`source` array, the default method is \"merge_nested\".\n\nIf both `linkMerge` and `pickValue` are null or not specified, and\nthere is only a single element in the `source`, then the input\nparameter takes the scalar value from the single input link (it is\n*not* wrapped in a single-list).\n\n* **merge_nested**\n\n  The input must be an array consisting of exactly one entry for each\n  input link.  If \"merge_nested\" is specified with a single link, the value\n  from the link must be wrapped in a single-item list.\n\n* **merge_flattened**\n\n  1. The source and sink parameters must be compatible types, or the source\n     type must be compatible with single element from the \"items\" type of\n     the destination array parameter.\n  2. Source parameters which are arrays are concatenated.\n     Source parameters which are single element types are appended as\n     single elements.\n\n# Picking non-null values among inbound data links\n\nIf present, `pickValue` specifies how to pick non-null values among inbound data links.\n\n`pickValue` is evaluated\n  1. Once all source values from upstream step or parameters are available.\n  2. After `linkMerge`.\n  3. Before `scatter` or `valueFrom`.\n\nThis is specifically intended to be useful in combination with\n[conditional execution](#WorkflowStep), where several upstream\nsteps may be connected to a single input (`source` is a list), and\nskipped steps produce null values.\n\nStatic type checkers should check for type consistency after inferring what the type\nwill be after `pickValue` is applied, just as they do currently for `linkMerge`.\n\n* **first_non_null**\n\n  For the first level of a list input, pick the first non-null element.  The result is a scalar.\n  It is an error if there is no non-null element.  Examples:\n  * `[null, x, null, y] -> x`\n  * `[null, [null], null, y] -> [null]`\n  * `[null, null, null] -> Runtime Error`\n\n  *Intended use case*: If-else pattern where the\n  value comes either from a conditional step or from a default or\n  fallback value. The conditional step(s) should be placed first in\n  the list.\n\n* **the_only_non_null**\n\n  For the first level of a list input, pick the single non-null element.  The result is a scalar.\n  It is an error if there is more than one non-null element.  Examples:\n\n  * `[null, x, null] -> x`\n  * `[null, x, null, y] -> Runtime Error`\n  * `[null, [null], null] -> [null]`\n  * `[null, null, null] -> Runtime Error`\n\n  *Intended use case*: Switch type patterns where developer considers\n  more than one active code path as a workflow error\n  (possibly indicating an error in writing `when` condition expressions).\n\n* **all_non_null**\n\n  For the first level of a list input, pick all non-null values.\n  The result is a list, which may be empty.  Examples:\n\n  * `[null, x, null] -> [x]`\n  * `[x, null, y] -> [x, y]`\n  * `[null, [x], [null]] -> [[x], [null]]`\n  * `[null, null, null] -> []`\n\n  *Intended use case*: It is valid to have more than one source, but\n   sources are conditional, so null sources (from skipped steps)\n   should be filtered out.","properties":{"default":{"description":"The default value for this parameter to use if either there is no\n`source` field, or the value produced by the `source` is `null`.  The\ndefault must be applied prior to scattering or evaluating `valueFrom`."},"id":{"description":"The unique identifier for this object.","type":"string"},"label":{"description":"A short, human-readable label of this object.","type":"string"},"linkMerge":{"description":"The method to use to merge multiple inbound links into a single array.\nIf not specified, the default method is \"merge_nested\".","enum":["merge_flattened","merge_nested"],"type":"string"},"loadContents":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nIf true, the file (or each file in the array) must be a UTF-8\ntext file 64 KiB or smaller, and the implementation must read\nthe entire contents of the file (or file array) and place it\nin the `contents` field of the File object for use by\nexpressions.  If the size of the file is greater than 64 KiB,\nthe implementation must raise a fatal error.","type":"boolean"},"loadListing":{"description":"Only valid when `type: Directory` or is an array of `items: Directory`.\n\nSpecify the desired behavior for loading the `listing` field of\na Directory object for use by expressions.\n\nThe order of precedence for loadListing is:\n\n  1. `loadListing` on an individual parameter\n  2. Inherited from `LoadListingRequirement`\n  3. By default: `no_listing`","enum":["deep_listing","no_listing","shallow_listing"],"type":"string"},"pickValue":{"description":"The method to use to choose non-null elements among multiple sources.","enum":["all_non_null","first_non_null","the_only_non_null"],"type":"string"},"source":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"Specifies one or more workflow parameters that will provide input to\nthe underlying step parameter."},"valueFrom":{"description":"To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must\nbe specified in the workflow or workflow step requirements.\n\nIf `valueFrom` is a constant string value, use this as the value for\nthis input parameter.\n\nIf `valueFrom` is a parameter reference or expression, it must be\nevaluated to yield the actual value to be assigned to the input field.\n\nThe `self` value in the parameter reference or expression must be\n1. `null` if there is no `source` field\n2. the value of the parameter(s) specified in the `source` field when this\nworkflow input parameter **is not** specified in this workflow step's `scatter` field.\n3. an element of the parameter specified in the `source` field when this workflow input\nparameter **is** specified in this workflow step's `scatter` field.\n\nThe value of `inputs` in the parameter reference or expression must be\nthe input object to the workflow step after assigning the `source`\nvalues, applying `default`, and then scattering.  The order of\nevaluating `valueFrom` among step input parameters is undefined and the\nresult of evaluating `valueFrom` on a parameter must not be visible to\nevaluation of `valueFrom` on other parameters.","type":"string"}},"required":[],"type":"object"},"WorkflowStepOutput":{"additionalProperties":false,"description":"Associate an output parameter of the underlying process with a workflow\nparameter.  The workflow parameter (given in the `id` field) be may be used\nas a `source` to connect with input parameters of other workflow steps, or\nwith an output parameter of the process.\n\nA unique identifier for this workflow output parameter.  This is\nthe identifier to use in the `source` field of `WorkflowStepInput`\nto connect the output value to downstream parameters.","properties":{"id":{"description":"The unique identifier for this object.","type":"string"}},"required":[],"type":"object"},"CWLImportManual":{"description":"Represents an '$import' directive that should point toward another compatible CWL file to import where specified. The contents of the imported file should be relevant contextually where it is being imported","$comment":"The schema validation of the CWL will not itself perform the '$import' to resolve and validate its contents. Therefore, the complete schema will not be validated entirely, and could still be partially malformed. To ensure proper and exhaustive validation of a CWL definition with this schema, all '$import' directives should be resolved and extended beforehand","type":"object","properties":{"$import":{"type":"string"}},"required":["$import"],"additionalProperties":false},"CWLIncludeManual":{"description":"Represents an '$include' directive that should point toward another compatible CWL file to import where specified. The contents of the imported file should be relevant contextually where it is being imported","$comment":"The schema validation of the CWL will not itself perform the '$include' to resolve and validate its contents. Therefore, the complete schema will not be validated entirely, and could still be partially malformed. To ensure proper and exhaustive validation of a CWL definition with this schema, all '$include' directives should be resolved and extended beforehand","type":"object","properties":{"$include":{"type":"string"}},"required":["$include"],"additionalProperties":false},"CWLDocumentMetadata":{"description":"Metadata for a CWL document","type":"object","properties":{"$namespaces":{"description":"The namespaces used in the document","type":"object","patternProperties":{"^[_a-zA-Z][a-zA-Z0-9_-]*$":{"type":"string"}}},"$schemas":{"description":"The schemas used in the document","type":"array","items":{"type":"string"}}},"patternProperties":{"^\\w+:.*$":{"type":"object"},"^\\w+:\\/\\/.*":{"type":"object"}},"required":[]},"CommandInputRecordFieldMap":{"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputRecordField","oneOf":[{"additionalProperties":false,"properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"format":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nThis must be one or more IRIs of concept nodes\nthat represents file formats which are allowed as input to this\nparameter, preferably defined within an ontology.  If no ontology is\navailable, file formats may be tested by exact match."},"inputBinding":{"$ref":"#/definitions/CommandLineBinding","description":"Describes how to turn this object into command line arguments."},"label":{"description":"A short, human-readable label of this object.","type":"string"},"loadContents":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nIf true, the file (or each file in the array) must be a UTF-8\ntext file 64 KiB or smaller, and the implementation must read\nthe entire contents of the file (or file array) and place it\nin the `contents` field of the File object for use by\nexpressions.  If the size of the file is greater than 64 KiB,\nthe implementation must raise a fatal error.","type":"boolean"},"loadListing":{"description":"Only valid when `type: Directory` or is an array of `items: Directory`.\n\nSpecify the desired behavior for loading the `listing` field of\na Directory object for use by expressions.\n\nThe order of precedence for loadListing is:\n\n  1. `loadListing` on an individual parameter\n  2. Inherited from `LoadListingRequirement`\n  3. By default: `no_listing`","enum":["deep_listing","no_listing","shallow_listing"],"type":"string"},"name":{"description":"The name of the field","type":"string"},"secondaryFiles":{"anyOf":[{"$ref":"#/definitions/SecondaryFileSchema"},{"items":{"$ref":"#/definitions/SecondaryFileSchema"},"type":"array"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nProvides a pattern or expression specifying files or\ndirectories that should be included alongside the primary\nfile.  Secondary files may be required or optional.  When not\nexplicitly specified, secondary files specified for `inputs`\nare required and `outputs` are optional.  An implementation\nmust include matching Files and Directories in the\n`secondaryFiles` property of the primary file.  These Files\nand Directories must be transferred and staged alongside the\nprimary file.  An implementation may fail workflow execution\nif a required secondary file does not exist.\n\nIf the value is an expression, the value of `self` in the expression\nmust be the primary input or output File object to which this binding\napplies.  The `basename`, `nameroot` and `nameext` fields must be\npresent in `self`.  For `CommandLineTool` outputs the `path` field must\nalso be present.  The expression must return a filename string relative\nto the path to the primary File, a File or Directory object with either\n`path` or `location` and `basename` fields set, or an array consisting\nof strings or File or Directory objects.  It is legal to reference an\nunchanged File or Directory object taken from input as a secondaryFile.\nThe expression may return \"null\" in which case there is no secondaryFile\nfrom that expression.\n\nTo work on non-filename-preserving storage systems, portable tool\ndescriptions should avoid constructing new values from `location`, but\nshould construct relative references using `basename` or `nameroot`\ninstead.\n\nIf a value in `secondaryFiles` is a string that is not an expression,\nit specifies that the following pattern should be applied to the path\nof the primary file to yield a filename relative to the primary File:\n\n  1. If string ends with `?` character, remove the last `?` and mark\n    the resulting secondary file as optional.\n  2. If string begins with one or more caret `^` characters, for each\n    caret, remove the last file extension from the path (the last\n    period `.` and all following characters).  If there are no file\n    extensions, the path is unchanged.\n  3. Append the remainder of the string to the end of the file path."},"streamable":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nA value of `true` indicates that the file is read or written\nsequentially without seeking.  An implementation may use this flag to\nindicate whether it is valid to stream file contents using a named\npipe.  Default: `false`.","type":"boolean"},"type":{"anyOf":[{"$ref":"#/definitions/CommandInputArraySchema"},{"$ref":"#/definitions/CommandInputRecordSchema"},{"$ref":"#/definitions/CommandInputEnumSchema"},{"items":{"anyOf":[{"$ref":"#/definitions/CommandInputArraySchema"},{"$ref":"#/definitions/CommandInputRecordSchema"},{"$ref":"#/definitions/CommandInputEnumSchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"The field type"}},"type":"object","required":["type"]},{"type":"array","items":{"anyOf":[{"$ref":"#/definitions/CommandInputArraySchema"},{"$ref":"#/definitions/CommandInputRecordSchema"},{"$ref":"#/definitions/CommandInputEnumSchema"},{"items":{"anyOf":[{"$ref":"#/definitions/CommandInputArraySchema"},{"$ref":"#/definitions/CommandInputRecordSchema"},{"$ref":"#/definitions/CommandInputEnumSchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"The field type"}},{"type":"string"}]},"InputRecordFieldMap":{"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordField","oneOf":[{"additionalProperties":false,"properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"format":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nThis must be one or more IRIs of concept nodes\nthat represents file formats which are allowed as input to this\nparameter, preferably defined within an ontology.  If no ontology is\navailable, file formats may be tested by exact match."},"label":{"description":"A short, human-readable label of this object.","type":"string"},"loadContents":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nIf true, the file (or each file in the array) must be a UTF-8\ntext file 64 KiB or smaller, and the implementation must read\nthe entire contents of the file (or file array) and place it\nin the `contents` field of the File object for use by\nexpressions.  If the size of the file is greater than 64 KiB,\nthe implementation must raise a fatal error.","type":"boolean"},"loadListing":{"description":"Only valid when `type: Directory` or is an array of `items: Directory`.\n\nSpecify the desired behavior for loading the `listing` field of\na Directory object for use by expressions.\n\nThe order of precedence for loadListing is:\n\n  1. `loadListing` on an individual parameter\n  2. Inherited from `LoadListingRequirement`\n  3. By default: `no_listing`","enum":["deep_listing","no_listing","shallow_listing"],"type":"string"},"name":{"description":"The name of the field","type":"string"},"secondaryFiles":{"anyOf":[{"$ref":"#/definitions/SecondaryFileSchema"},{"items":{"$ref":"#/definitions/SecondaryFileSchema"},"type":"array"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nProvides a pattern or expression specifying files or\ndirectories that should be included alongside the primary\nfile.  Secondary files may be required or optional.  When not\nexplicitly specified, secondary files specified for `inputs`\nare required and `outputs` are optional.  An implementation\nmust include matching Files and Directories in the\n`secondaryFiles` property of the primary file.  These Files\nand Directories must be transferred and staged alongside the\nprimary file.  An implementation may fail workflow execution\nif a required secondary file does not exist.\n\nIf the value is an expression, the value of `self` in the expression\nmust be the primary input or output File object to which this binding\napplies.  The `basename`, `nameroot` and `nameext` fields must be\npresent in `self`.  For `CommandLineTool` outputs the `path` field must\nalso be present.  The expression must return a filename string relative\nto the path to the primary File, a File or Directory object with either\n`path` or `location` and `basename` fields set, or an array consisting\nof strings or File or Directory objects.  It is legal to reference an\nunchanged File or Directory object taken from input as a secondaryFile.\nThe expression may return \"null\" in which case there is no secondaryFile\nfrom that expression.\n\nTo work on non-filename-preserving storage systems, portable tool\ndescriptions should avoid constructing new values from `location`, but\nshould construct relative references using `basename` or `nameroot`\ninstead.\n\nIf a value in `secondaryFiles` is a string that is not an expression,\nit specifies that the following pattern should be applied to the path\nof the primary file to yield a filename relative to the primary File:\n\n  1. If string ends with `?` character, remove the last `?` and mark\n    the resulting secondary file as optional.\n  2. If string begins with one or more caret `^` characters, for each\n    caret, remove the last file extension from the path (the last\n    period `.` and all following characters).  If there are no file\n    extensions, the path is unchanged.\n  3. Append the remainder of the string to the end of the file path."},"streamable":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nA value of `true` indicates that the file is read or written\nsequentially without seeking.  An implementation may use this flag to\nindicate whether it is valid to stream file contents using a named\npipe.  Default: `false`.","type":"boolean"},"type":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"The field type"}},"type":"object","required":["type"]},{"type":"array","items":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/InputRecordSchema"},{"$ref":"#/definitions/InputEnumSchema"},{"$ref":"#/definitions/InputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"The field type"}},{"type":"string"}]},"CommandOutputRecordFieldMap":{"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordField","oneOf":[{"additionalProperties":false,"properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"format":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nThis is the file format that will be assigned to the output\nFile object.","type":"string"},"label":{"description":"A short, human-readable label of this object.","type":"string"},"name":{"description":"The name of the field","type":"string"},"outputBinding":{"$ref":"#/definitions/CommandOutputBinding","description":"Describes how to generate this output object based on the files\nproduced by a CommandLineTool"},"secondaryFiles":{"anyOf":[{"$ref":"#/definitions/SecondaryFileSchema"},{"items":{"$ref":"#/definitions/SecondaryFileSchema"},"type":"array"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nProvides a pattern or expression specifying files or\ndirectories that should be included alongside the primary\nfile.  Secondary files may be required or optional.  When not\nexplicitly specified, secondary files specified for `inputs`\nare required and `outputs` are optional.  An implementation\nmust include matching Files and Directories in the\n`secondaryFiles` property of the primary file.  These Files\nand Directories must be transferred and staged alongside the\nprimary file.  An implementation may fail workflow execution\nif a required secondary file does not exist.\n\nIf the value is an expression, the value of `self` in the expression\nmust be the primary input or output File object to which this binding\napplies.  The `basename`, `nameroot` and `nameext` fields must be\npresent in `self`.  For `CommandLineTool` outputs the `path` field must\nalso be present.  The expression must return a filename string relative\nto the path to the primary File, a File or Directory object with either\n`path` or `location` and `basename` fields set, or an array consisting\nof strings or File or Directory objects.  It is legal to reference an\nunchanged File or Directory object taken from input as a secondaryFile.\nThe expression may return \"null\" in which case there is no secondaryFile\nfrom that expression.\n\nTo work on non-filename-preserving storage systems, portable tool\ndescriptions should avoid constructing new values from `location`, but\nshould construct relative references using `basename` or `nameroot`\ninstead.\n\nIf a value in `secondaryFiles` is a string that is not an expression,\nit specifies that the following pattern should be applied to the path\nof the primary file to yield a filename relative to the primary File:\n\n  1. If string ends with `?` character, remove the last `?` and mark\n    the resulting secondary file as optional.\n  2. If string begins with one or more caret `^` characters, for each\n    caret, remove the last file extension from the path (the last\n    period `.` and all following characters).  If there are no file\n    extensions, the path is unchanged.\n  3. Append the remainder of the string to the end of the file path."},"streamable":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nA value of `true` indicates that the file is read or written\nsequentially without seeking.  An implementation may use this flag to\nindicate whether it is valid to stream file contents using a named\npipe.  Default: `false`.","type":"boolean"},"type":{"anyOf":[{"$ref":"#/definitions/CommandOutputArraySchema"},{"$ref":"#/definitions/CommandOutputRecordSchema"},{"$ref":"#/definitions/CommandOutputEnumSchema"},{"items":{"anyOf":[{"$ref":"#/definitions/CommandOutputArraySchema"},{"$ref":"#/definitions/CommandOutputRecordSchema"},{"$ref":"#/definitions/CommandOutputEnumSchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"The field type"}},"type":"object","required":["type"]},{"type":"array","items":{"anyOf":[{"$ref":"#/definitions/CommandOutputArraySchema"},{"$ref":"#/definitions/CommandOutputRecordSchema"},{"$ref":"#/definitions/CommandOutputEnumSchema"},{"items":{"anyOf":[{"$ref":"#/definitions/CommandOutputArraySchema"},{"$ref":"#/definitions/CommandOutputRecordSchema"},{"$ref":"#/definitions/CommandOutputEnumSchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"The field type"}},{"type":"string"}]},"OutputRecordFieldMap":{"description":"Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordField","oneOf":[{"additionalProperties":false,"properties":{"doc":{"anyOf":[{"items":{"type":"string"},"type":"array"},{"type":"string"}],"description":"A documentation string for this object, or an array of strings which should be concatenated."},"format":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nThis is the file format that will be assigned to the output\nFile object.","type":"string"},"label":{"description":"A short, human-readable label of this object.","type":"string"},"name":{"description":"The name of the field","type":"string"},"secondaryFiles":{"anyOf":[{"$ref":"#/definitions/SecondaryFileSchema"},{"items":{"$ref":"#/definitions/SecondaryFileSchema"},"type":"array"}],"description":"Only valid when `type: File` or is an array of `items: File`.\n\nProvides a pattern or expression specifying files or\ndirectories that should be included alongside the primary\nfile.  Secondary files may be required or optional.  When not\nexplicitly specified, secondary files specified for `inputs`\nare required and `outputs` are optional.  An implementation\nmust include matching Files and Directories in the\n`secondaryFiles` property of the primary file.  These Files\nand Directories must be transferred and staged alongside the\nprimary file.  An implementation may fail workflow execution\nif a required secondary file does not exist.\n\nIf the value is an expression, the value of `self` in the expression\nmust be the primary input or output File object to which this binding\napplies.  The `basename`, `nameroot` and `nameext` fields must be\npresent in `self`.  For `CommandLineTool` outputs the `path` field must\nalso be present.  The expression must return a filename string relative\nto the path to the primary File, a File or Directory object with either\n`path` or `location` and `basename` fields set, or an array consisting\nof strings or File or Directory objects.  It is legal to reference an\nunchanged File or Directory object taken from input as a secondaryFile.\nThe expression may return \"null\" in which case there is no secondaryFile\nfrom that expression.\n\nTo work on non-filename-preserving storage systems, portable tool\ndescriptions should avoid constructing new values from `location`, but\nshould construct relative references using `basename` or `nameroot`\ninstead.\n\nIf a value in `secondaryFiles` is a string that is not an expression,\nit specifies that the following pattern should be applied to the path\nof the primary file to yield a filename relative to the primary File:\n\n  1. If string ends with `?` character, remove the last `?` and mark\n    the resulting secondary file as optional.\n  2. If string begins with one or more caret `^` characters, for each\n    caret, remove the last file extension from the path (the last\n    period `.` and all following characters).  If there are no file\n    extensions, the path is unchanged.\n  3. Append the remainder of the string to the end of the file path."},"streamable":{"description":"Only valid when `type: File` or is an array of `items: File`.\n\nA value of `true` indicates that the file is read or written\nsequentially without seeking.  An implementation may use this flag to\nindicate whether it is valid to stream file contents using a named\npipe.  Default: `false`.","type":"boolean"},"type":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"The field type"}},"type":"object","required":["type"]},{"type":"array","items":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"items":{"anyOf":[{"$ref":"#/definitions/OutputRecordSchema"},{"$ref":"#/definitions/OutputEnumSchema"},{"$ref":"#/definitions/OutputArraySchema"},{"type":"string"}]},"type":"array"},{"type":"string"}],"description":"The field type"}},{"type":"string"}]},"InlineJavascriptRequirementMap":{"type":"object","properties":{"expressionLib":{"description":"Additional code fragments that will also be inserted\nbefore executing the expression code.  Allows for function definitions that may\nbe called from CWL expressions.","items":{"anyOf":[{"type":"string"},{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"}]},"type":"array"}},"required":[],"description":"Indicates that the workflow platform must support inline Javascript expressions.\nIf this requirement is not present, the workflow platform must not perform expression\ninterpolation."},"SchemaDefRequirementMap":{"type":"object","properties":{"types":{"description":"The list of type definitions.","items":{"anyOf":[{"anyOf":[{"$ref":"#/definitions/CommandInputArraySchema"},{"$ref":"#/definitions/CommandInputRecordSchema"},{"$ref":"#/definitions/CommandInputEnumSchema"}]},{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"}]},"type":"array"}},"required":["types"],"description":"This field consists of an array of type definitions which must be used when\ninterpreting the `inputs` and `outputs` fields.  When a `type` field\ncontains a IRI, the implementation must check if the type is defined in\n`schemaDefs` and use that definition.  If the type is not found in\n`schemaDefs`, it is an error.  The entries in `schemaDefs` must be\nprocessed in the order listed such that later schema definitions may refer\nto earlier schema definitions.\n\n- **Type definitions are allowed for `enum` and `record` types only.**\n- Type definitions may be shared by defining them in a file and then\n  `$include`-ing them in the `types` field.\n- A file can contain a list of type definitions"},"LoadListingRequirementMap":{"type":"object","properties":{"loadListing":{"enum":["deep_listing","no_listing","shallow_listing"],"type":"string"}},"required":[],"description":"Specify the desired behavior for loading the `listing` field of\na Directory object for use by expressions."},"DockerRequirementMap":{"type":"object","properties":{"dockerFile":{"description":"Supply the contents of a Dockerfile which will be built using `docker build`.","type":"string"},"dockerImageId":{"description":"The image id that will be used for `docker run`.  May be a\nhuman-readable image name or the image identifier hash.  May be skipped\nif `dockerPull` is specified, in which case the `dockerPull` image id\nmust be used.","type":"string"},"dockerImport":{"description":"Provide HTTP URL to download and gunzip a Docker images using `docker import.","type":"string"},"dockerLoad":{"description":"Specify an HTTP URL from which to download a Docker image using `docker load`.","type":"string"},"dockerOutputDirectory":{"description":"Set the designated output directory to a specific location inside the\nDocker container.","type":"string"},"dockerPull":{"description":"Specify a Docker image to retrieve using `docker pull`. Can contain the\nimmutable digest to ensure an exact container is used:\n`dockerPull: ubuntu@sha256:45b23dee08af5e43a7fea6c4cf9c25ccf269ee113168c19722f87876677c5cb2`","type":"string"}},"required":[],"description":"Indicates that a workflow component should be run in a\n[Docker](https://docker.com) or Docker-compatible (such as\n[Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment and\nspecifies how to fetch or build the image.\n\nIf a CommandLineTool lists `DockerRequirement` under\n`hints` (or `requirements`), it may (or must) be run in the specified Docker\ncontainer.\n\nThe platform must first acquire or install the correct Docker image as\nspecified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`.\n\nThe platform must execute the tool in the container using `docker run` with\nthe appropriate Docker image and tool command line.\n\nThe workflow platform may provide input files and the designated output\ndirectory through the use of volume bind mounts.  The platform should rewrite\nfile paths in the input object to correspond to the Docker bind mounted\nlocations. That is, the platform should rewrite values in the parameter context\nsuch as `runtime.outdir`, `runtime.tmpdir` and others to be valid paths\nwithin the container. The platform must ensure that `runtime.outdir` and\n`runtime.tmpdir` are distinct directories.\n\nWhen running a tool contained in Docker, the workflow platform must not\nassume anything about the contents of the Docker container, such as the\npresence or absence of specific software, except to assume that the\ngenerated command line represents a valid command within the runtime\nenvironment of the container.\n\nA container image may specify an\n[ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint)\nand/or\n[CMD](https://docs.docker.com/engine/reference/builder/#cmd).\nCommand line arguments will be appended after all elements of\nENTRYPOINT, and will override all elements specified using CMD (in\nother words, CMD is only used when the CommandLineTool definition\nproduces an empty command line).\n\nUse of implicit ENTRYPOINT or CMD are discouraged due to reproducibility\nconcerns of the implicit hidden execution point (For further discussion, see\n[https://doi.org/10.12688/f1000research.15140.1](https://doi.org/10.12688/f1000research.15140.1)). Portable\nCommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD.\nCommandLineTools which do rely on ENTRYPOINT or CMD must list `DockerRequirement` in the\n`requirements` section.\n\n## Interaction with other requirements\n\nIf [EnvVarRequirement](#EnvVarRequirement) is specified alongside a\nDockerRequirement, the environment variables must be provided to Docker\nusing `--env` or `--env-file` and interact with the container's preexisting\nenvironment as defined by Docker."},"SoftwareRequirementMap":{"type":"object","properties":{"packages":{"description":"The list of software to be configured.","items":{"anyOf":[{"$ref":"#/definitions/SoftwarePackage"},{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"}]},"type":"array"}},"required":["packages"],"description":"A list of software packages that should be configured in the environment of\nthe defined process."},"InitialWorkDirRequirementMap":{"type":"object","properties":{"listing":{"anyOf":[{"items":{"anyOf":[{"anyOf":[{"$ref":"#/definitions/Directory"},{"$ref":"#/definitions/File"},{"items":{"anyOf":[{"anyOf":[{"$ref":"#/definitions/Directory"},{"$ref":"#/definitions/File"}]},{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"}]},"type":"array"},{"$ref":"#/definitions/Dirent"},{"type":"string"}]},{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"}]},"type":"array"},{"type":"string"}],"description":"The list of files or subdirectories that must be staged prior\nto executing the command line tool.\n\nReturn type of each expression must validate as `[\"null\",\nFile, Directory, Dirent, {type: array, items: [File,\nDirectory]}]`.\n\nEach `File` or `Directory` that is returned by an Expression\nmust be added to the designated output directory prior to\nexecuting the tool.\n\nEach `Dirent` record that is listed or returned by an\nexpression specifies a file to be created or staged in the\ndesignated output directory prior to executing the tool.\n\nExpressions may return null, in which case they have no effect.\n\nFiles or Directories which are listed in the input parameters\nand appear in the `InitialWorkDirRequirement` listing must\nhave their `path` set to their staged location.  If the same\nFile or Directory appears more than once in the\n`InitialWorkDirRequirement` listing, the implementation must\nchoose exactly one value for `path`; how this value is chosen\nis undefined."}},"required":[],"description":"Define a list of files and subdirectories that must be staged by the workflow platform prior to executing the command line tool.\nNormally files are staged within the designated output directory. However, when running inside containers, files may be staged at arbitrary locations, see discussion for [`Dirent.entryname`](#Dirent). Together with `DockerRequirement.dockerOutputDirectory` it is possible to control the locations of both input and output files when running in containers."},"EnvVarRequirementMap":{"type":"object","properties":{"envDef":{"description":"The list of environment variables.","oneOf":[{"items":{"anyOf":[{"$ref":"#/definitions/EnvironmentDef"},{"$ref":"#/definitions/CWLImportManual"},{"$ref":"#/definitions/CWLIncludeManual"}]},"type":"array"},{"patternProperties":{"^[_a-zA-Z][a-zA-Z0-9_-]*$":{"type":"string"}}}]}},"required":["envDef"],"description":"Define a list of environment variables which will be set in the\nexecution environment of the tool.  See `EnvironmentDef` for details."},"ShellCommandRequirementMap":{"type":"object","properties":{},"required":[],"description":"Modify the behavior of CommandLineTool to generate a single string\ncontaining a shell command line.  Each item in the `arguments` list must\nbe joined into a string separated by single spaces and quoted to prevent\ninterpretation by the shell, unless `CommandLineBinding` for that argument\ncontains `shellQuote: false`.  If `shellQuote: false` is specified, the\nargument is joined into the command string without quoting, which allows\nthe use of shell metacharacters such as `|` for pipes."},"ResourceRequirementMap":{"type":"object","properties":{"coresMax":{"description":"Maximum reserved number of CPU cores.\n\nSee `coresMin` for discussion about fractional CPU requests.","type":["string","number"]},"coresMin":{"description":"Minimum reserved number of CPU cores (default is 1).\n\nMay be a fractional value to indicate to a scheduling\nalgorithm that one core can be allocated to multiple\njobs. For example, a value of 0.25 indicates that up to 4\njobs may run in parallel on 1 core.  A value of 1.25 means\nthat up to 3 jobs can run on a 4 core system (4/1.25 \u2248 3).\n\nProcesses can only share a core allocation if the sum of each\nof their `ramMax`, `tmpdirMax`, and `outdirMax` requests also\ndo not exceed the capacity of the node.\n\nProcesses sharing a core must have the same level of isolation\n(typically a container or VM) that they would normally have.\n\nThe reported number of CPU cores reserved for the process,\nwhich is available to expressions on the CommandLineTool as\n`runtime.cores`, must be a non-zero integer, and may be\ncalculated by rounding up the cores request to the next whole\nnumber.\n\nScheduling systems may allocate fractional CPU resources by\nsetting quotas or scheduling weights.  Scheduling systems that\ndo not support fractional CPUs may round up the request to the\nnext whole number.","type":["string","number"]},"outdirMax":{"description":"Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)\n\nSee `outdirMin` for discussion about fractional storage requests.","type":["string","number"]},"outdirMin":{"description":"Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) (default is 1024)\n\nMay be a fractional value.  If so, the actual storage request\nmust be rounded up to the next whole number.  The reported\namount of storage reserved for the process, which is available\nto expressions on the CommandLineTool as `runtime.outdirSize`,\nmust be a non-zero integer.","type":["string","number"]},"ramMax":{"description":"Maximum reserved RAM in mebibytes (2**20)\n\nSee `ramMin` for discussion about fractional RAM requests.","type":["string","number"]},"ramMin":{"description":"Minimum reserved RAM in mebibytes (2**20) (default is 256)\n\nMay be a fractional value.  If so, the actual RAM request must\nbe rounded up to the next whole number.  The reported amount of\nRAM reserved for the process, which is available to\nexpressions on the CommandLineTool as `runtime.ram`, must be a\nnon-zero integer.","type":["string","number"]},"tmpdirMax":{"description":"Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)\n\nSee `tmpdirMin` for discussion about fractional storage requests.","type":["string","number"]},"tmpdirMin":{"description":"Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) (default is 1024)\n\nMay be a fractional value.  If so, the actual storage request\nmust be rounded up to the next whole number.  The reported\namount of storage reserved for the process, which is available\nto expressions on the CommandLineTool as `runtime.tmpdirSize`,\nmust be a non-zero integer.","type":["string","number"]}},"required":[],"description":"Specify basic hardware resource requirements.\n\n\"min\" is the minimum amount of a resource that must be reserved to\nschedule a job. If \"min\" cannot be satisfied, the job should not\nbe run.\n\n\"max\" is the maximum amount of a resource that the job shall be\nallocated. If a node has sufficient resources, multiple jobs may\nbe scheduled on a single node provided each job's \"max\" resource\nrequirements are met. If a job attempts to exceed its resource\nallocation, an implementation may deny additional resources, which\nmay result in job failure.\n\nIf both \"min\" and \"max\" are specified, an implementation may\nchoose to allocate any amount between \"min\" and \"max\", with the\nactual allocation provided in the `runtime` object.\n\nIf \"min\" is specified but \"max\" is not, then \"max\" == \"min\"\nIf \"max\" is specified by \"min\" is not, then \"min\" == \"max\".\n\nIt is an error if max < min.\n\nIt is an error if the value of any of these fields is negative.\n\nIf neither \"min\" nor \"max\" is specified for a resource, use the default values below."},"WorkReuseMap":{"type":"object","properties":{"enableReuse":{"type":["string","boolean"]}},"required":["enableReuse"],"description":"For implementations that support reusing output from past work (on\nthe assumption that same code and same input produce same\nresults), control whether to enable or disable the reuse behavior\nfor a particular tool or step (to accommodate situations where that\nassumption is incorrect).  A reused step is not executed but\ninstead returns the same output as the original execution.\n\nIf `WorkReuse` is not specified, correct tools should assume it\nis enabled by default."},"NetworkAccessMap":{"type":"object","properties":{"networkAccess":{"type":["string","boolean"]}},"required":["networkAccess"],"description":"Indicate whether a process requires outgoing IPv4/IPv6 network\naccess.  Choice of IPv4 or IPv6 is implementation and site\nspecific, correct tools must support both.\n\nIf `networkAccess` is false or not specified, tools must not\nassume network access, except for localhost (the loopback device).\n\nIf `networkAccess` is true, the tool must be able to make outgoing\nconnections to network resources.  Resources may be on a private\nsubnet or the public Internet.  However, implementations and sites\nmay apply their own security policies to restrict what is\naccessible by the tool.\n\nEnabling network access does not imply a publicly routable IP\naddress or the ability to accept inbound connections."},"InplaceUpdateRequirementMap":{"type":"object","properties":{"inplaceUpdate":{"type":"boolean"}},"required":["inplaceUpdate"],"description":"\nIf `inplaceUpdate` is true, then an implementation supporting this\nfeature may permit tools to directly update files with `writable:\ntrue` in InitialWorkDirRequirement.  That is, as an optimization,\nfiles may be destructively modified in place as opposed to copied\nand updated.\n\nAn implementation must ensure that only one workflow step may\naccess a writable file at a time.  It is an error if a file which\nis writable by one workflow step file is accessed (for reading or\nwriting) by any other workflow step running independently.\nHowever, a file which has been updated in a previous completed\nstep may be used as input to multiple steps, provided it is\nread-only in every step.\n\nWorkflow steps which modify a file must produce the modified file\nas output.  Downstream steps which further process the file must\nuse the output of previous steps, and not refer to a common input\n(this is necessary for both ordering and correctness).\n\nWorkflow authors should provide this in the `hints` section.  The\nintent of this feature is that workflows produce the same results\nwhether or not InplaceUpdateRequirement is supported by the\nimplementation, and this feature is primarily available as an\noptimization for particular environments.\n\nUsers and implementers should be aware that workflows that\ndestructively modify inputs may not be repeatable or reproducible.\nIn particular, enabling this feature implies that WorkReuse should\nnot be enabled."},"ToolTimeLimitMap":{"type":"object","properties":{"timelimit":{"description":"The time limit, in seconds.  A time limit of zero means no\ntime limit.  Negative time limits are an error.","type":["string","number"]}},"required":["timelimit"],"description":"Set an upper limit on the execution time of a CommandLineTool.\nA CommandLineTool whose execution duration exceeds the time\nlimit may be preemptively terminated and considered failed.\nMay also be used by batch systems to make scheduling decisions.\nThe execution duration excludes external operations, such as\nstaging of files, pulling a docker image etc, and only counts\nwall-time for the execution of the command line itself."},"SubworkflowFeatureRequirementMap":{"type":"object","properties":{},"required":[],"description":"Indicates that the workflow platform must support nested workflows in\nthe `run` field of [WorkflowStep](#WorkflowStep)."},"ScatterFeatureRequirementMap":{"type":"object","properties":{},"required":[],"description":"Indicates that the workflow platform must support the `scatter` and\n`scatterMethod` fields of [WorkflowStep](#WorkflowStep)."},"MultipleInputFeatureRequirementMap":{"type":"object","properties":{},"required":[],"description":"Indicates that the workflow platform must support multiple inbound data links\nlisted in the `source` field of [WorkflowStepInput](#WorkflowStepInput)."},"StepInputExpressionRequirementMap":{"type":"object","properties":{},"required":[],"description":"Indicate that the workflow platform must support the `valueFrom` field\nof [WorkflowStepInput](#WorkflowStepInput)."},"CWLFile":{"type":"object","allOf":[{"oneOf":[{"$ref":"#/definitions/Workflow"},{"$ref":"#/definitions/CommandLineTool"},{"$ref":"#/definitions/ExpressionTool"}]},{"oneOf":[{"$ref":"#/definitions/CWLDocumentMetadata"}]}],"properties":{"inputs":true,"stdout":true,"hints":true,"temporaryFailCodes":true,"doc":true,"$schemas":true,"requirements":true,"cwlVersion":true,"successCodes":true,"baseCommand":true,"permanentFailCodes":true,"id":true,"expression":true,"steps":true,"stdin":true,"intent":true,"arguments":true,"stderr":true,"outputs":true,"$namespaces":true,"class":true,"label":true},"patternProperties":{"^\\w+:.*$":{"type":"object"},"^\\w+:\\/\\/.*":{"type":"object"}},"additionalProperties":false},"CWLGraph":{"type":"object","properties":{"$graph":{"type":"array","items":{"$ref":"#/definitions/CWLFile"}},"cwlVersion":{"description":"CWL document version. Always required at the document root. Not\nrequired for a Process embedded inside another Process.","enum":["draft-2","draft-3","draft-3.dev1","draft-3.dev2","draft-3.dev3","draft-3.dev4","draft-3.dev5","draft-4.dev1","draft-4.dev2","draft-4.dev3","v1.0","v1.0.dev4","v1.1","v1.1.0-dev1","v1.2","v1.2.0-dev1","v1.2.0-dev2","v1.2.0-dev3","v1.2.0-dev4","v1.2.0-dev5"],"type":"string"}},"required":["$graph"]},"CWLGraphOrFile":{"type":"object","additionalProperties":false,"allOf":[{"oneOf":[{"$ref":"#/definitions/CWLGraph"},{"$ref":"#/definitions/CWLFile"}]},{"$ref":"#/definitions/CWLDocumentMetadata"}],"properties":{"inputs":true,"stdout":true,"hints":true,"temporaryFailCodes":true,"doc":true,"$schemas":true,"requirements":true,"cwlVersion":true,"successCodes":true,"baseCommand":true,"permanentFailCodes":true,"id":true,"expression":true,"steps":true,"stdin":true,"intent":true,"$graph":true,"arguments":true,"stderr":true,"outputs":true,"$namespaces":true,"class":true,"label":true},"patternProperties":{"^\\w+:.*$":{"type":"object"},"^\\w+:\\/\\/.*":{"type":"object"}}}}}
</schema>

[User] Provide a JSON object that satisfies the schema "cwl_schema". Here are the required top‑level fields: none (all optional). Return only the valid JSON object.

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputArraySchema

A documentation string for this object, or an array of strings which should be concatenated.

Describes how to turn this object into command line arguments.

Defines the type of the array elements.

A short, human-readable label of this object.

The identifier for this type

Must be `array`

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputEnumSchema

The identifier for this type

Defines the set of valid symbols.

Must be `enum`

An input parameter for a CommandLineTool.

The default value to use for this parameter if the parameter is missing
from the input object, or if the value of the parameter in the input
object is `null`.  Default values are applied before evaluating expressions
(e.g. dependent `valueFrom` fields).

Only valid when `type: File` or is an array of `items: File`.

This must be one or more IRIs of concept nodes
that represents file formats which are allowed as input to this
parameter, preferably defined within an ontology.  If no ontology is
available, file formats may be tested by exact match.

The unique identifier for this object.

Describes how to turn the input parameters of a process into
command line arguments.

Only valid when `type: File` or is an array of `items: File`.

If true, the file (or each file in the array) must be a UTF-8
text file 64 KiB or smaller, and the implementation must read
the entire contents of the file (or file array) and place it
in the `contents` field of the File object for use by
expressions.  If the size of the file is greater than 64 KiB,
the implementation must raise a fatal error.

Only valid when `type: Directory` or is an array of `items: Directory`.

Specify the desired behavior for loading the `listing` field of
a Directory object for use by expressions.

The order of precedence for loadListing is:

  1. `loadListing` on an individual parameter
  2. Inherited from `LoadListingRequirement`
  3. By default: `no_listing`

Only valid when `type: File` or is an array of `items: File`.

Provides a pattern or expression specifying files or
directories that should be included alongside the primary
file.  Secondary files may be required or optional.  When not
explicitly specified, secondary files specified for `inputs`
are required and `outputs` are optional.  An implementation
must include matching Files and Directories in the
`secondaryFiles` property of the primary file.  These Files
and Directories must be transferred and staged alongside the
primary file.  An implementation may fail workflow execution
if a required secondary file does not exist.

If the value is an expression, the value of `self` in the expression
must be the primary input or output File object to which this binding
applies.  The `basename`, `nameroot` and `nameext` fields must be
present in `self`.  For `CommandLineTool` outputs the `path` field must
also be present.  The expression must return a filename string relative
to the path to the primary File, a File or Directory object with either
`path` or `location` and `basename` fields set, or an array consisting
of strings or File or Directory objects.  It is legal to reference an
unchanged File or Directory object taken from input as a secondaryFile.
The expression may return "null" in which case there is no secondaryFile
from that expression.

To work on non-filename-preserving storage systems, portable tool
descriptions should avoid constructing new values from `location`, but
should construct relative references using `basename` or `nameroot`
instead.

If a value in `secondaryFiles` is a string that is not an expression,
it specifies that the following pattern should be applied to the path
of the primary file to yield a filename relative to the primary File:

  1. If string ends with `?` character, remove the last `?` and mark
    the resulting secondary file as optional.
  2. If string begins with one or more caret `^` characters, for each
    caret, remove the last file extension from the path (the last
    period `.` and all following characters).  If there are no file
    extensions, the path is unchanged.
  3. Append the remainder of the string to the end of the file path.

Only valid when `type: File` or is an array of `items: File`.

A value of `true` indicates that the file is read or written
sequentially without seeking.  An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe.  Default: `false`.

Specify valid types of data that may be assigned to this parameter.

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputRecordField

The name of the field

The field type

The field type

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputRecordSchema

Defines the fields of the record.

The identifier for this type

Must be `record`

When listed under `inputBinding` in the input schema, the term
"value" refers to the corresponding value in the input object.  For
binding objects listed in `CommandLineTool.arguments`, the term "value"
refers to the effective value after evaluating `valueFrom`.

The binding behavior when building the command line depends on the data
type of the value.  If there is a mismatch between the type described by
the input schema and the effective value, such as resulting from an
expression evaluation, an implementation must use the data type of the
effective value.

  - **string**: Add `prefix` and the string to the command line.

  - **number**: Add `prefix` and decimal representation to command line.

  - **boolean**: If true, add `prefix` to the command line.  If false, add
      nothing.

  - **File**: Add `prefix` and the value of
    [`File.path`](#File) to the command line.

  - **Directory**: Add `prefix` and the value of
    [`Directory.path`](#Directory) to the command line.

  - **array**: If `itemSeparator` is specified, add `prefix` and the join
      the array into a single string with `itemSeparator` separating the
      items.  Otherwise, first add `prefix`, then recursively process
      individual elements.
      If the array is empty, it does not add anything to command line.

  - **object**: Add `prefix` only, and recursively add object fields for
      which `inputBinding` is specified.

  - **null**: Add nothing.

Join the array elements into a single string with the elements
separated by `itemSeparator`.

Use of `loadContents` in `InputBinding` is deprecated.
Preserved for v1.0 backwards compatibility.  Will be removed in
CWL v2.0.  Use `InputParameter.loadContents` instead.

The sorting key.  Default position is 0. If a [CWL Parameter Reference](#Parameter_references)
or [CWL Expression](#Expressions_(Optional)) is used and if the
inputBinding is associated with an input parameter, then the value of
`self` will be the value of the input parameter.  Input parameter
defaults (as specified by the `InputParameter.default` field) must be
applied before evaluating the expression. Expressions must return a
single value of type int or a null.

Command line prefix to add before the value.

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.

If `ShellCommandRequirement` is in the requirements for the current command,
this controls whether the value is quoted on the command line (default is true).
Use `shellQuote: false` to inject metacharacters for operations such as pipes.

If `shellQuote` is true or not provided, the implementation must not
permit interpretation of any shell metacharacters or directives.

If `valueFrom` is a constant string value, use this as the value and
apply the binding rules above.

If `valueFrom` is an expression, evaluate the expression to yield the
actual value to use to build the command line and apply the binding
rules above.  If the inputBinding is associated with an input
parameter, the value of `self` in the expression will be the value of
the input parameter.  Input parameter defaults (as specified by the
`InputParameter.default` field) must be applied before evaluating the
expression.

If the value of the associated input parameter is `null`, `valueFrom` is
not evaluated and nothing is added to the command line.

When a binding is part of the `CommandLineTool.arguments` field,
the `valueFrom` field is required.

This defines the schema of the CWL Command Line Tool Description document.

Command line bindings which are not directly associated with input
parameters. If the value is a string, it is used as a string literal
argument. If it is an Expression, the result of the evaluation is used
as an argument.

Specifies the program to execute.  If an array, the first element of
the array is the command to execute, and subsequent elements are
mandatory command line arguments.  The elements in `baseCommand` must
appear before any command line bindings from `inputBinding` or
`arguments`.

If `baseCommand` is not provided or is an empty array, the first
element of the command line produced after processing `inputBinding` or
`arguments` must be used as the program to execute.

If the program includes a path separator character it must
be an absolute path, otherwise it is an error.  If the program does not
include a path separator, search the `$PATH` variable in the runtime
environment of the workflow runner find the absolute path of the
executable.

CWL document version. Always required at the document root. Not
required for a Process embedded inside another Process.

A documentation string for this object, or an array of strings which should be concatenated.

Declares requirements that apply to either the runtime environment or the
workflow engine that must be met in order to execute this process.  If
an implementation cannot satisfy all requirements, or a requirement is
listed which is not recognized by the implementation, it is a fatal
error and the implementation must not attempt to run the process,
unless overridden at user option.

The unique identifier for this object.

Only useful for `$graph` at `Process` level. Should not be exposed
to users in graphical or terminal user interfaces.

Defines the input parameters of the process.  The process is ready to
run when all required input parameters are associated with concrete
values.  Input parameters include a schema for each parameter which is
used to validate the input object.  It may also be used to build a user
interface for constructing the input object.

When accepting an input object, all input parameters must have a value.
If an input parameter is missing from the input object, it must be
assigned a value of `null` (or the value of `default` for that
parameter, if provided) for the purposes of validation and evaluation
of expressions.

Specify valid types of data that may be assigned to this parameter.

An identifier for the type of computational operation, of this Process.
Especially useful for [`Operation`](Workflow.html#Operation), but can also be used for
[`CommandLineTool`](CommandLineTool.html#CommandLineTool),
[`Workflow`](Workflow.html#Workflow), or [ExpressionTool](Workflow.html#ExpressionTool).

If provided, then this must be an IRI of a concept node that
represents the type of operation, preferably defined within an ontology.

For example, in the domain of bioinformatics, one can use an IRI from
the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004),
like [Alignment](http://edamontology.org/operation_2928),
or [Clustering](http://edamontology.org/operation_3432); or a more
specific Operation concept like
[Split read mapping](http://edamontology.org/operation_3199).

A short, human-readable label of this object.

Defines the parameters representing the output of the process.  May be
used to generate and/or validate the output object.

Specify valid types of data that may be assigned to this parameter.

Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail.
If not specified, all exit codes except 0 are considered permanent failure.

Declares requirements that apply to either the runtime environment or the
workflow engine that must be met in order to execute this process.  If
an implementation cannot satisfy all requirements, or a requirement is
listed which is not recognized by the implementation, it is a fatal
error and the implementation must not attempt to run the process,
unless overridden at user option.

Capture the command's standard error stream to a file written to
the designated output directory.

If `stderr` is a string, it specifies the file name to use.

If `stderr` is an expression, the expression is evaluated and must
return a string with the file name to use to capture stderr.  If the
return value is not a string, or the resulting path contains illegal
characters (such as the path separator `/`) it is an error.

A path to a file whose contents must be piped into the command's
standard input stream.

Capture the command's standard output stream to a file written to
the designated output directory.

If the `CommandLineTool` contains logically chained commands
(e.g. `echo a && echo b`) `stdout` must include the output of
every command.

If `stdout` is a string, it specifies the file name to use.

If `stdout` is an expression, the expression is evaluated and must
return a string with the file name to use to capture stdout.  If the
return value is not a string, or the resulting path contains illegal
characters (such as the path separator `/`) it is an error.

Exit codes that indicate the process completed successfully.

If not specified, only exit code 0 is considered success.

Exit codes that indicate the process failed due to a possibly
temporary condition, where executing the process with the same
runtime environment and inputs may produce different results.

If not specified, no exit codes are considered temporary failure.

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputArraySchema

A documentation string for this object, or an array of strings which should be concatenated.

Defines the type of the array elements.

A short, human-readable label of this object.

The identifier for this type

Must be `array`

Describes how to generate an output parameter based on the files produced
by a CommandLineTool.

The output parameter value is generated by applying these operations in the
following order:

  - glob
  - loadContents
  - outputEval
  - secondaryFiles

Find files or directories relative to the output directory, using POSIX
glob(3) pathname matching.  If an array is provided, find files or
directories that match any pattern in the array.  If an expression is
provided, the expression must return a string or an array of strings,
which will then be evaluated as one or more glob patterns.  Must only
match and return files/directories which actually exist.

If the value of glob is a relative path pattern (does not
begin with a slash '/') then it is resolved relative to the
output directory.  If the value of the glob is an absolute
path pattern (it does begin with a slash '/') then it must
refer to a path within the output directory.  It is an error
if any glob resolves to a path outside the output directory.
Specifically this means globs that resolve to paths outside the output
directory are illegal.

A glob may match a path within the output directory which is
actually a symlink to another file.  In this case, the
expected behavior is for the resulting File/Directory object to take the
`basename` (and corresponding `nameroot` and `nameext`) of the
symlink.  The `location` of the File/Directory is implementation
dependent, but logically the File/Directory should have the same content
as the symlink target.  Platforms may stage output files/directories to
cloud storage that lack the concept of a symlink.  In
this case file content and directories may be duplicated, or (to avoid
duplication) the File/Directory `location` may refer to the symlink
target.

It is an error if a symlink in the output directory (or any
symlink in a chain of links) refers to any file or directory
that is not under an input or output directory.

Implementations may shut down a container before globbing
output, so globs and expressions must not assume access to the
container filesystem except for declared input and output.

Only valid when `type: File` or is an array of `items: File`.

If true, the file (or each file in the array) must be a UTF-8
text file 64 KiB or smaller, and the implementation must read
the entire contents of the file (or file array) and place it
in the `contents` field of the File object for use by
expressions.  If the size of the file is greater than 64 KiB,
the implementation must raise a fatal error.

Only valid when `type: Directory` or is an array of `items: Directory`.

Specify the desired behavior for loading the `listing` field of
a Directory object for use by expressions.

The order of precedence for loadListing is:

  1. `loadListing` on an individual parameter
  2. Inherited from `LoadListingRequirement`
  3. By default: `no_listing`

Evaluate an expression to generate the output value.  If
`glob` was specified, the value of `self` must be an array
containing file objects that were matched.  If no files were
matched, `self` must be a zero length array; if a single file
was matched, the value of `self` is an array of a single
element.  The exit code of the process is
available in the expression as `runtime.exitCode`.

Additionally, if `loadContents` is true, the file must be a
UTF-8 text file 64 KiB or smaller, and the implementation must
read the entire contents of the file (or file array) and place
it in the `contents` field of the File object for use in
`outputEval`.  If the size of the file is greater than 64 KiB,
the implementation must raise a fatal error.

If a tool needs to return a large amount of structured data to
the workflow, loading the output object from `cwl.output.json`
bypasses `outputEval` and is not subject to the 64 KiB
`loadContents` limit.

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputEnumSchema

The identifier for this type

Defines the set of valid symbols.

Must be `enum`

An output parameter for a CommandLineTool.

Only valid when `type: File` or is an array of `items: File`.

This is the file format that will be assigned to the output
File object.

The unique identifier for this object.

Describes how to generate this output object based on the files produced by a CommandLineTool

Only valid when `type: File` or is an array of `items: File`.

A value of `true` indicates that the file is read or written
sequentially without seeking.  An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe.  Default: `false`.

Specify valid types of data that may be assigned to this parameter.

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordField

The name of the field

Describes how to generate this output object based on the files
produced by a CommandLineTool

The field type

The field type

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordSchema

A documentation string for this object, or an array of strings which should be concatenated.

Defines the fields of the record.

A short, human-readable label of this object.

The identifier for this type

Must be `record`

Represents a directory to present to a command line tool.

Directories are represented as objects with `class` of `Directory`.  Directory objects have
a number of properties that provide metadata about the directory.

The `location` property of a Directory is a IRI that uniquely identifies
the directory.  Implementations must support the file:// IRI scheme and may
support other schemes such as http://.  Alternately to `location`,
implementations must also accept the `path` property on Directory, which
must be a filesystem path available on the same host as the CWL runner (for
inputs) or the runtime environment of a command line tool execution (for
command line tool outputs).

A Directory object may have a `listing` field.  This is a list of File and
Directory objects that are contained in the Directory.  For each entry in
`listing`, the `basename` property defines the name of the File or
Subdirectory when staged to disk.  If `listing` is not provided, the
implementation must have some way of fetching the Directory listing at
runtime based on the `location` field.

If a Directory does not have `location`, it is a Directory literal.  A
Directory literal must provide `listing`.  Directory literals must be
created on disk at runtime as needed.

The resources in a Directory literal do not need to have any implied
relationship in their `location`.  For example, a Directory listing may
contain two files located on different hosts.  It is the responsibility of
the runtime to ensure that those files are staged to disk appropriately.
Secondary files associated with files in `listing` must also be staged to
the same Directory.

When executing a CommandLineTool, Directories must be recursively staged
first and have local values of `path` assigned.

Directory objects in CommandLineTool output must provide either a
`location` IRI or a `path` property in the context of the tool execution
runtime (local to the compute node, or within the executing container).

An ExpressionTool may forward file references from input to output by using
the same value for `location`.

Name conflicts (the same `basename` appearing multiple times in `listing`
or in any entry in `secondaryFiles` in the listing) is a fatal error.

The base name of the directory, that is, the name of the file without any
leading directory path.  The base name must not contain a slash `/`.

If not provided, the implementation must set this field based on the
`location` field by taking the final path component after parsing
`location` as an IRI.  If `basename` is provided, it is not required to
match the value from `location`.

When this file is made available to a CommandLineTool, it must be named
with `basename`, i.e. the final component of the `path` field must match
`basename`.

Must be `Directory` to indicate this object describes a Directory.

List of files or subdirectories contained in this directory.  The name
of each file or subdirectory is determined by the `basename` field of
each `File` or `Directory` object.  It is an error if a `File` shares a
`basename` with any other entry in `listing`.  If two or more
`Directory` object share the same `basename`, this must be treated as
equivalent to a single subdirectory with the listings recursively
merged.

An IRI that identifies the directory resource.  This may be a relative
reference, in which case it must be resolved using the base IRI of the
document.  The location may refer to a local or remote resource.  If
the `listing` field is not set, the implementation must use the
location IRI to retrieve directory listing.  If an implementation is
unable to retrieve the directory listing stored at a remote resource (due to
unsupported protocol, access denied, or other issue) it must signal an
error.

If the `location` field is not provided, the `listing` field must be
provided.  The implementation must assign a unique identifier for
the `location` field.

If the `path` field is provided but the `location` field is not, an
implementation may assign the value of the `path` field to `location`,
then follow the rules above.

The local path where the Directory is made available prior to executing a
CommandLineTool.  This must be set by the implementation.  This field
must not be used in any other context.  The command line tool being
executed must be able to access the directory at `path` using the POSIX
`opendir(2)` syscall.

If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
(`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,
`<space>`, `<tab>`, and `<newline>`) or characters
[not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)
for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)
then implementations may terminate the process with a
`permanentFailure`.

Define a file or subdirectory that must be staged to a particular
place prior to executing the command line tool.  May be the result
of executing an expression, such as building a configuration file
from a template.

Usually files are staged within the [designated output directory](#Runtime_environment).
However, under certain circumstances, files may be staged at
arbitrary locations, see discussion for `entryname`.

If the value is a string literal or an expression which evaluates to a
string, a new text file must be created with the string as the file contents.

If the value is an expression that evaluates to a `File` or
`Directory` object, or an array of `File` or `Directory`
objects, this indicates the referenced file or directory
should be added to the designated output directory prior to
executing the tool.

If the value is an expression that evaluates to `null`,
nothing is added to the designated output directory, the entry
has no effect.

If the value is an expression that evaluates to some other
array, number, or object not consisting of `File` or
`Directory` objects, a new file must be created with the value
serialized to JSON text as the file contents.  The JSON
serialization behavior should match the behavior of string
interpolation of [Parameter
references](#Parameter_references).

The "target" name of the file or subdirectory.  If `entry` is
a File or Directory, the `entryname` field overrides the value
of `basename` of the File or Directory object.

* Required when `entry` evaluates to file contents only
* Optional when `entry` evaluates to a File or Directory object with a `basename`
* Invalid when `entry` evaluates to an array of File or Directory objects.

If `entryname` is a relative path, it specifies a name within
the designated output directory.  A relative path starting
with `../` or that resolves to location above the designated output directory is an error.

If `entryname` is an absolute path (starts with a slash `/`)
it is an error unless the following conditions are met:

  * `DockerRequirement` is present in `requirements`
  * The program is will run inside a software container
  where, from the perspective of the program, the root
  filesystem is not shared with any other user or
  running program.

In this case, and the above conditions are met, then
`entryname` may specify the absolute path within the container
where the file or directory must be placed.

If true, the File or Directory (or array of Files or
Directories) declared in `entry` must be writable by the tool.

Changes to the file or directory must be isolated and not
visible by any other CommandLineTool process.  This may be
implemented by making a copy of the original file or
directory.

Disruptive changes to the referenced file or directory must not
be allowed unless `InplaceUpdateRequirement.inplaceUpdate` is true.

Default false (files and directories read-only by default).

A directory marked as `writable: true` implies that all files and
subdirectories are recursively writable as well.

If `writable` is false, the file may be made available using a
bind mount or file system link to avoid unnecessary copying of
the input file.  Command line tools may receive an error on
attempting to rename or delete files or directories that are
not explicitly marked as writable.

Indicates that a workflow component should be run in a
[Docker](https://docker.com) or Docker-compatible (such as
[Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment and
specifies how to fetch or build the image.

If a CommandLineTool lists `DockerRequirement` under
`hints` (or `requirements`), it may (or must) be run in the specified Docker
container.

The platform must first acquire or install the correct Docker image as
specified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`.

The platform must execute the tool in the container using `docker run` with
the appropriate Docker image and tool command line.

The workflow platform may provide input files and the designated output
directory through the use of volume bind mounts.  The platform should rewrite
file paths in the input object to correspond to the Docker bind mounted
locations. That is, the platform should rewrite values in the parameter context
such as `runtime.outdir`, `runtime.tmpdir` and others to be valid paths
within the container. The platform must ensure that `runtime.outdir` and
`runtime.tmpdir` are distinct directories.

When running a tool contained in Docker, the workflow platform must not
assume anything about the contents of the Docker container, such as the
presence or absence of specific software, except to assume that the
generated command line represents a valid command within the runtime
environment of the container.

A container image may specify an
[ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint)
and/or
[CMD](https://docs.docker.com/engine/reference/builder/#cmd).
Command line arguments will be appended after all elements of
ENTRYPOINT, and will override all elements specified using CMD (in
other words, CMD is only used when the CommandLineTool definition
produces an empty command line).

Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility
concerns of the implicit hidden execution point (For further discussion, see
[https://doi.org/10.12688/f1000research.15140.1](https://doi.org/10.12688/f1000research.15140.1)). Portable
CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD.
CommandLineTools which do rely on ENTRYPOINT or CMD must list `DockerRequirement` in the
`requirements` section.

## Interaction with other requirements

If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a
DockerRequirement, the environment variables must be provided to Docker
using `--env` or `--env-file` and interact with the container's preexisting
environment as defined by Docker.

Always 'DockerRequirement'

Supply the contents of a Dockerfile which will be built using `docker build`.

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.

Provide HTTP URL to download and gunzip a Docker images using `docker import.

Specify an HTTP URL from which to download a Docker image using `docker load`.

Set the designated output directory to a specific location inside the
Docker container.

Specify a Docker image to retrieve using `docker pull`. Can contain the
immutable digest to ensure an exact container is used:
`dockerPull: ubuntu@sha256:45b23dee08af5e43a7fea6c4cf9c25ccf269ee113168c19722f87876677c5cb2`

Define a list of environment variables which will be set in the
execution environment of the tool.  See `EnvironmentDef` for details.

Always 'EnvVarRequirement'

The list of environment variables.

Define an environment variable that will be set in the runtime environment
by the workflow platform when executing the command line tool.  May be the
result of executing an expression, such as getting a parameter from input.

The environment variable name

The environment variable value

An ExpressionTool is a type of Process object that can be run by itself
or as a Workflow step. It executes a pure Javascript expression that has
access to the same input parameters as a workflow. It is meant to be used
sparingly as a way to isolate complex Javascript expressions that need to
operate on input data and produce some result; perhaps just a
rearrangement of the inputs. No Docker software container is required
or allowed.

CWL document version. Always required at the document root. Not
required for a Process embedded inside another Process.

A documentation string for this object, or an array of strings which should be concatenated.

The expression to execute.  The expression must return a plain
Javascript object which matches the output parameters of the
ExpressionTool.

Declares requirements that apply to either the runtime environment or the
workflow engine that must be met in order to execute this process.  If
an implementation cannot satisfy all requirements, or a requirement is
listed which is not recognized by the implementation, it is a fatal
error and the implementation must not attempt to run the process,
unless overridden at user option.

The unique identifier for this object.

Only useful for `$graph` at `Process` level. Should not be exposed
to users in graphical or terminal user interfaces.

Specify valid types of data that may be assigned to this parameter.

A short, human-readable label of this object.

Defines the parameters representing the output of the process.  May be
used to generate and/or validate the output object.

Specify valid types of data that may be assigned to this parameter.
Note that this field just acts as a hint, as the outputs of an
ExpressionTool process are always considered valid.

Declares requirements that apply to either the runtime environment or the
workflow engine that must be met in order to execute this process.  If
an implementation cannot satisfy all requirements, or a requirement is
listed which is not recognized by the implementation, it is a fatal
error and the implementation must not attempt to run the process,
unless overridden at user option.

Auto-generated class implementation for https://w3id.org/cwl/cwl#ExpressionToolOutputParameter

A documentation string for this object, or an array of strings which should be concatenated.

Only valid when `type: File` or is an array of `items: File`.

This is the file format that will be assigned to the output
File object.

The unique identifier for this object.

A short, human-readable label of this object.

Only valid when `type: File` or is an array of `items: File`.

A value of `true` indicates that the file is read or written
sequentially without seeking.  An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe.  Default: `false`.

Specify valid types of data that may be assigned to this parameter.
Note that this field just acts as a hint, as the outputs of an
ExpressionTool process are always considered valid.

Represents a file (or group of files when `secondaryFiles` is provided) that
will be accessible by tools using standard POSIX file system call API such as
open(2) and read(2).

Files are represented as objects with `class` of `File`.  File objects have
a number of properties that provide metadata about the file.

The `location` property of a File is a IRI that uniquely identifies the
file.  Implementations must support the `file://` IRI scheme and may support
other schemes such as `http://` and `https://`.  The value of `location` may also be a
relative reference, in which case it must be resolved relative to the IRI
of the document it appears in.  Alternately to `location`, implementations
must also accept the `path` property on File, which must be a filesystem
path available on the same host as the CWL runner (for inputs) or the
runtime environment of a command line tool execution (for command line tool
outputs).

If no `location` or `path` is specified, a file object must specify
`contents` with the UTF-8 text content of the file.  This is a "file
literal".  File literals do not correspond to external resources, but are
created on disk with `contents` with when needed for executing a tool.
Where appropriate, expressions can return file literals to define new files
on a runtime.  The maximum size of `contents` is 64 kilobytes.

The `basename` property defines the filename on disk where the file is
staged.  This may differ from the resource name.  If not provided,
`basename` must be computed from the last path part of `location` and made
available to expressions.

The `secondaryFiles` property is a list of File or Directory objects that
must be staged in the same directory as the primary file.  It is an error
for file names to be duplicated in `secondaryFiles`.

The `size` property is the size in bytes of the File.  It must be computed
from the resource and made available to expressions.  The `checksum` field
contains a cryptographic hash of the file content for use it verifying file
contents.  Implementations may, at user option, enable or disable
computation of the `checksum` field for performance or other reasons.
However, the ability to compute output checksums is required to pass the
CWL conformance test suite.

When executing a CommandLineTool, the files and secondary files may be
staged to an arbitrary directory, but must use the value of `basename` for
the filename.  The `path` property must be file path in the context of the
tool execution runtime (local to the compute node, or within the executing
container).  All computed properties should be available to expressions.
File literals also must be staged and `path` must be set.

When collecting CommandLineTool outputs, `glob` matching returns file paths
(with the `path` property) and the derived properties. This can all be
modified by `outputEval`.  Alternately, if the file `cwl.output.json` is
present in the output, `outputBinding` is ignored.

File objects in the output must provide either a `location` IRI or a `path`
property in the context of the tool execution runtime (local to the compute
node, or within the executing container).

When evaluating an ExpressionTool, file objects must be referenced via
`location` (the expression tool does not have access to files on disk so
`path` is meaningless) or as file literals.  It is legal to return a file
object with an existing `location` but a different `basename`.  The
`loadContents` field of ExpressionTool inputs behaves the same as on
CommandLineTool inputs, however it is not meaningful on the outputs.

An ExpressionTool may forward file references from input to output by using
the same value for `location`.

The base name of the file, that is, the name of the file without any
leading directory path.  The base name must not contain a slash `/`.

If not provided, the implementation must set this field based on the
`location` field by taking the final path component after parsing
`location` as an IRI.  If `basename` is provided, it is not required to
match the value from `location`.

When this file is made available to a CommandLineTool, it must be named
with `basename`, i.e. the final component of the `path` field must match
`basename`.

Optional hash code for validating file integrity.  Currently, must be in the form
"sha1$ + hexadecimal string" using the SHA-1 algorithm.

Must be `File` to indicate this object describes a file.

File contents literal.

If neither `location` nor `path` is provided, `contents` must be
non-null.  The implementation must assign a unique identifier for the
`location` field.  When the file is staged as input to CommandLineTool,
the value of `contents` must be written to a file.

If `contents` is set as a result of a Javascript expression,
an `entry` in `InitialWorkDirRequirement`, or read in from
`cwl.output.json`, there is no specified upper limit on the
size of `contents`.  Implementations may have practical limits
on the size of `contents` based on memory and storage
available to the workflow runner or other factors.

If the `loadContents` field of an `InputParameter` or
`OutputParameter` is true, and the input or output File object
`location` is valid, the file must be a UTF-8 text file 64 KiB
or smaller, and the implementation must read the entire
contents of the file and place it in the `contents` field.  If
the size of the file is greater than 64 KiB, the
implementation must raise a fatal error.

The name of the directory containing file, that is, the path leading up
to the final slash in the path such that `dirname + '/' + basename ==
path`.

The implementation must set this field based on the value of `path`
prior to evaluating parameter references or expressions in a
CommandLineTool document.  This field must not be used in any other
context.

The format of the file: this must be an IRI of a concept node that
represents the file format, preferably defined within an ontology.
If no ontology is available, file formats may be tested by exact match.

Reasoning about format compatibility must be done by checking that an
input file format is the same, `owl:equivalentClass` or
`rdfs:subClassOf` the format required by the input parameter.
`owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if
`<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer
`<C> owl:subclassOf <A>`.

File format ontologies may be provided in the "$schemas" metadata at the
root of the document.  If no ontologies are specified in `$schemas`, the
runtime may perform exact file format matches.

An IRI that identifies the file resource.  This may be a relative
reference, in which case it must be resolved using the base IRI of the
document.  The location may refer to a local or remote resource; the
implementation must use the IRI to retrieve file content.  If an
implementation is unable to retrieve the file content stored at a
remote resource (due to unsupported protocol, access denied, or other
issue) it must signal an error.

If the `location` field is not provided, the `contents` field must be
provided.  The implementation must assign a unique identifier for
the `location` field.

If the `path` field is provided but the `location` field is not, an
implementation may assign the value of the `path` field to `location`,
then follow the rules above.

The basename extension such that `nameroot + nameext == basename`, and
`nameext` is empty or begins with a period and contains at most one
period.  Leading periods on the basename are ignored; a basename of
`.cshrc` will have an empty `nameext`.

The implementation must set this field automatically based on the value
of `basename` prior to evaluating parameter references or expressions.

The basename root such that `nameroot + nameext == basename`, and
`nameext` is empty or begins with a period and contains at most one
period.  For the purposes of path splitting leading periods on the
basename are ignored; a basename of `.cshrc` will have a nameroot of
`.cshrc`.

The implementation must set this field automatically based on the value
of `basename` prior to evaluating parameter references or expressions.

The local host path where the File is available when a CommandLineTool is
executed.  This field must be set by the implementation.  The final
path component must match the value of `basename`.  This field
must not be used in any other context.  The command line tool being
executed must be able to access the file at `path` using the POSIX
`open(2)` syscall.

As a special case, if the `path` field is provided but the `location`
field is not, an implementation may assign the value of the `path`
field to `location`, and remove the `path` field.

If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
(`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,
`<space>`, `<tab>`, and `<newline>`) or characters
[not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)
for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)
then implementations may terminate the process with a
`permanentFailure`.

A list of additional files or directories that are associated with the
primary file and must be transferred alongside the primary file.
Examples include indexes of the primary file, or external references
which must be included when loading primary document.  A file object
listed in `secondaryFiles` may itself include `secondaryFiles` for
which the same rules apply.

Optional file size (in bytes)

Define a list of files and subdirectories that must be staged by the workflow platform prior to executing the command line tool.
Normally files are staged within the designated output directory. However, when running inside containers, files may be staged at arbitrary locations, see discussion for [`Dirent.entryname`](#Dirent). Together with `DockerRequirement.dockerOutputDirectory` it is possible to control the locations of both input and output files when running in containers.

InitialWorkDirRequirement

The list of files or subdirectories that must be staged prior
to executing the command line tool.

Return type of each expression must validate as `["null",
File, Directory, Dirent, {type: array, items: [File,
Directory]}]`.

Each `File` or `Directory` that is returned by an Expression
must be added to the designated output directory prior to
executing the tool.

Each `Dirent` record that is listed or returned by an
expression specifies a file to be created or staged in the
designated output directory prior to executing the tool.

Expressions may return null, in which case they have no effect.

Files or Directories which are listed in the input parameters
and appear in the `InitialWorkDirRequirement` listing must
have their `path` set to their staged location.  If the same
File or Directory appears more than once in the
`InitialWorkDirRequirement` listing, the implementation must
choose exactly one value for `path`; how this value is chosen
is undefined.

Indicates that the workflow platform must support inline Javascript expressions.
If this requirement is not present, the workflow platform must not perform expression
interpolation.

Always 'InlineJavascriptRequirement'

Additional code fragments that will also be inserted
before executing the expression code.  Allows for function definitions that may
be called from CWL expressions.

If `inplaceUpdate` is true, then an implementation supporting this
feature may permit tools to directly update files with `writable:
true` in InitialWorkDirRequirement.  That is, as an optimization,
files may be destructively modified in place as opposed to copied
and updated.

An implementation must ensure that only one workflow step may
access a writable file at a time.  It is an error if a file which
is writable by one workflow step file is accessed (for reading or
writing) by any other workflow step running independently.
However, a file which has been updated in a previous completed
step may be used as input to multiple steps, provided it is
read-only in every step.

Workflow steps which modify a file must produce the modified file
as output.  Downstream steps which further process the file must
use the output of previous steps, and not refer to a common input
(this is necessary for both ordering and correctness).

Workflow authors should provide this in the `hints` section.  The
intent of this feature is that workflows produce the same results
whether or not InplaceUpdateRequirement is supported by the
implementation, and this feature is primarily available as an
optimization for particular environments.

Users and implementers should be aware that workflows that
destructively modify inputs may not be repeatable or reproducible.
In particular, enabling this feature implies that WorkReuse should
not be enabled.

Always 'InplaceUpdateRequirement'

Auto-generated class implementation for https://w3id.org/cwl/cwl#InputArraySchema

A documentation string for this object, or an array of strings which should be concatenated.

Defines the type of the array elements.

A short, human-readable label of this object.

The identifier for this type

Must be `array`

Auto-generated class implementation for https://w3id.org/cwl/cwl#InputBinding

Use of `loadContents` in `InputBinding` is deprecated.
Preserved for v1.0 backwards compatibility.  Will be removed in
CWL v2.0.  Use `InputParameter.loadContents` instead.

Auto-generated class implementation for https://w3id.org/cwl/cwl#InputEnumSchema

The identifier for this type

Defines the set of valid symbols.

Must be `enum`

Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordField

Only valid when `type: File` or is an array of `items: File`.

This must be one or more IRIs of concept nodes
that represents file formats which are allowed as input to this
parameter, preferably defined within an ontology.  If no ontology is
available, file formats may be tested by exact match.

Only valid when `type: File` or is an array of `items: File`.

If true, the file (or each file in the array) must be a UTF-8
text file 64 KiB or smaller, and the implementation must read
the entire contents of the file (or file array) and place it
in the `contents` field of the File object for use by
expressions.  If the size of the file is greater than 64 KiB,
the implementation must raise a fatal error.

Only valid when `type: Directory` or is an array of `items: Directory`.

Specify the desired behavior for loading the `listing` field of
a Directory object for use by expressions.

The order of precedence for loadListing is:

  1. `loadListing` on an individual parameter
  2. Inherited from `LoadListingRequirement`
  3. By default: `no_listing`

The name of the field

Only valid when `type: File` or is an array of `items: File`.

A value of `true` indicates that the file is read or written
sequentially without seeking.  An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe.  Default: `false`.

The field type

The field type

Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordSchema

Defines the fields of the record.

The identifier for this type

Must be `record`

Specify the desired behavior for loading the `listing` field of
a Directory object for use by expressions.

Always 'LoadListingRequirement'

Indicates that the workflow platform must support multiple inbound data links
listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput).

Always 'MultipleInputFeatureRequirement'

Indicate whether a process requires outgoing IPv4/IPv6 network
access.  Choice of IPv4 or IPv6 is implementation and site
specific, correct tools must support both.

If `networkAccess` is false or not specified, tools must not
assume network access, except for localhost (the loopback device).

If `networkAccess` is true, the tool must be able to make outgoing
connections to network resources.  Resources may be on a private
subnet or the public Internet.  However, implementations and sites
may apply their own security policies to restrict what is
accessible by the tool.

Enabling network access does not imply a publicly routable IP
address or the ability to accept inbound connections.

Always 'NetworkAccess'

This record describes an abstract operation.  It is a potential
step of a workflow that has not yet been bound to a concrete
implementation.  It specifies an input and output signature, but
does not provide enough information to be executed.  An
implementation (or other tooling) may provide a means of binding
an Operation to a concrete process (such as Workflow,
CommandLineTool, or ExpressionTool) with a compatible signature.

CWL document version. Always required at the document root. Not
required for a Process embedded inside another Process.

A documentation string for this object, or an array of strings which should be concatenated.

Declares requirements that apply to either the runtime environment or the
workflow engine that must be met in order to execute this process.  If
an implementation cannot satisfy all requirements, or a requirement is
listed which is not recognized by the implementation, it is a fatal
error and the implementation must not attempt to run the process,
unless overridden at user option.

The unique identifier for this object.

Only useful for `$graph` at `Process` level. Should not be exposed
to users in graphical or terminal user interfaces.

Specify valid types of data that may be assigned to this parameter.

A short, human-readable label of this object.

Defines the parameters representing the output of the process.  May be
used to generate and/or validate the output object.

Specify valid types of data that may be assigned to this parameter.

Declares requirements that apply to either the runtime environment or the
workflow engine that must be met in order to execute this process.  If
an implementation cannot satisfy all requirements, or a requirement is
listed which is not recognized by the implementation, it is a fatal
error and the implementation must not attempt to run the process,
unless overridden at user option.

Describe an input parameter of an operation.

The default value to use for this parameter if the parameter is missing
from the input object, or if the value of the parameter in the input
object is `null`.  Default values are applied before evaluating expressions
(e.g. dependent `valueFrom` fields).

A documentation string for this object, or an array of strings which should be concatenated.

The unique identifier for this object.

A short, human-readable label of this object.

Specify valid types of data that may be assigned to this parameter.

Describe an output parameter of an operation.

Only valid when `type: File` or is an array of `items: File`.

This is the file format that will be assigned to the output
File object.

The unique identifier for this object.

Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputArraySchema

Defines the type of the array elements.

The identifier for this type

Must be `array`

Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputEnumSchema

The identifier for this type

Defines the set of valid symbols.

Must be `enum`

Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordField

The name of the field

Only valid when `type: File` or is an array of `items: File`.

A value of `true` indicates that the file is read or written
sequentially without seeking.  An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe.  Default: `false`.

The field type

The field type

Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordSchema

Defines the fields of the record.

The identifier for this type

Must be `record`

Specify basic hardware resource requirements.

"min" is the minimum amount of a resource that must be reserved to
schedule a job. If "min" cannot be satisfied, the job should not
be run.

"max" is the maximum amount of a resource that the job shall be
allocated. If a node has sufficient resources, multiple jobs may
be scheduled on a single node provided each job's "max" resource
requirements are met. If a job attempts to exceed its resource
allocation, an implementation may deny additional resources, which
may result in job failure.

If both "min" and "max" are specified, an implementation may
choose to allocate any amount between "min" and "max", with the
actual allocation provided in the `runtime` object.

If "min" is specified but "max" is not, then "max" == "min"
If "max" is specified by "min" is not, then "min" == "max".

It is an error if max < min.

It is an error if the value of any of these fields is negative.

If neither "min" nor "max" is specified for a resource, use the default values below.

Always 'ResourceRequirement'

Maximum reserved number of CPU cores.

See `coresMin` for discussion about fractional CPU requests.

Minimum reserved number of CPU cores (default is 1).

May be a fractional value to indicate to a scheduling
algorithm that one core can be allocated to multiple
jobs. For example, a value of 0.25 indicates that up to 4
jobs may run in parallel on 1 core.  A value of 1.25 means
that up to 3 jobs can run on a 4 core system (4/1.25 ≈ 3).

Processes can only share a core allocation if the sum of each
of their `ramMax`, `tmpdirMax`, and `outdirMax` requests also
do not exceed the capacity of the node.

Processes sharing a core must have the same level of isolation
(typically a container or VM) that they would normally have.

The reported number of CPU cores reserved for the process,
which is available to expressions on the CommandLineTool as
`runtime.cores`, must be a non-zero integer, and may be
calculated by rounding up the cores request to the next whole
number.

Scheduling systems may allocate fractional CPU resources by
setting quotas or scheduling weights.  Scheduling systems that
do not support fractional CPUs may round up the request to the
next whole number.

Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)

See `outdirMin` for discussion about fractional storage requests.

Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) (default is 1024)

May be a fractional value.  If so, the actual storage request
must be rounded up to the next whole number.  The reported
amount of storage reserved for the process, which is available
to expressions on the CommandLineTool as `runtime.outdirSize`,
must be a non-zero integer.

Maximum reserved RAM in mebibytes (2**20)

See `ramMin` for discussion about fractional RAM requests.

Minimum reserved RAM in mebibytes (2**20) (default is 256)

May be a fractional value.  If so, the actual RAM request must
be rounded up to the next whole number.  The reported amount of
RAM reserved for the process, which is available to
expressions on the CommandLineTool as `runtime.ram`, must be a
non-zero integer.

Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)

See `tmpdirMin` for discussion about fractional storage requests.

Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) (default is 1024)

May be a fractional value.  If so, the actual storage request
must be rounded up to the next whole number.  The reported
amount of storage reserved for the process, which is available
to expressions on the CommandLineTool as `runtime.tmpdirSize`,
must be a non-zero integer.

Indicates that the workflow platform must support the `scatter` and
`scatterMethod` fields of [WorkflowStep](#WorkflowStep).

Always 'ScatterFeatureRequirement'

This field consists of an array of type definitions which must be used when
interpreting the `inputs` and `outputs` fields.  When a `type` field
contains a IRI, the implementation must check if the type is defined in
`schemaDefs` and use that definition.  If the type is not found in
`schemaDefs`, it is an error.  The entries in `schemaDefs` must be
processed in the order listed such that later schema definitions may refer
to earlier schema definitions.

- **Type definitions are allowed for `enum` and `record` types only.**
- Type definitions may be shared by defining them in a file and then
  `$include`-ing them in the `types` field.
- A file can contain a list of type definitions

Always 'SchemaDefRequirement'

The list of type definitions.

Secondary files are specified using the following micro-DSL for secondary files:

* If the value is a string, it is transformed to an object with two fields
  `pattern` and `required`
* By default, the value of `required` is `null`
  (this indicates default behavior, which may be based on the context)
* If the value ends with a question mark `?` the question mark is
  stripped off and the value of the field `required` is set to `False`
* The remaining value is assigned to the field `pattern`

For implementation details and examples, please see
[this section](SchemaSalad.html#Domain_Specific_Language_for_secondary_files)
in the Schema Salad specification.

Provides a pattern or expression specifying files or directories that
should be included alongside the primary file.

If the value is an expression, the value of `self` in the
expression must be the primary input or output File object to
which this binding applies.  The `basename`, `nameroot` and
`nameext` fields must be present in `self`.  For
`CommandLineTool` inputs the `location` field must also be
present.  For `CommandLineTool` outputs the `path` field must
also be present.  If secondary files were included on an input
File object as part of the Process invocation, they must also
be present in `secondaryFiles` on `self`.

The expression must return either: a filename string relative
to the path to the primary File, a File or Directory object
(`class: File` or `class: Directory`) with either `location`
(for inputs) or `path` (for outputs) and `basename` fields
set, or an array consisting of strings or File or Directory
objects as previously described.

It is legal to use `location` from a File or Directory object
passed in as input, including `location` from secondary files
on `self`.  If an expression returns a File object with the
same `location` but a different `basename` as a secondary file
that was passed in, the expression result takes precedence.
Setting the basename with an expression this way affects the
`path` where the secondary file will be staged to in the
CommandLineTool.

The expression may return "null" in which case there is no
secondary file from that expression.

To work on non-filename-preserving storage systems, portable
tool descriptions should treat `location` as an
[opaque identifier](#opaque-strings) and avoid constructing new
values from `location`, but should construct relative references
using `basename` or `nameroot` instead, or propagate `location`
from defined inputs.

If a value in `secondaryFiles` is a string that is not an expression,
it specifies that the following pattern should be applied to the path
of the primary file to yield a filename relative to the primary File:

  1. If string ends with `?` character, remove the last `?` and mark
    the resulting secondary file as optional.
  2. If string begins with one or more caret `^` characters, for each
    caret, remove the last file extension from the path (the last
    period `.` and all following characters).  If there are no file
    extensions, the path is unchanged.
  3. Append the remainder of the string to the end of the file path.

An implementation must not fail workflow execution if `required` is
set to `false` and the expected secondary file does not exist.
Default value for `required` field is `true` for secondary files on
input and `false` for secondary files on output.

Modify the behavior of CommandLineTool to generate a single string
containing a shell command line.  Each item in the `arguments` list must
be joined into a string separated by single spaces and quoted to prevent
interpretation by the shell, unless `CommandLineBinding` for that argument
contains `shellQuote: false`.  If `shellQuote: false` is specified, the
argument is joined into the command string without quoting, which allows
the use of shell metacharacters such as `|` for pipes.

Always 'ShellCommandRequirement'

Auto-generated class implementation for https://w3id.org/cwl/cwl#SoftwarePackage

The name of the software to be made available. If the name is
common, inconsistent, or otherwise ambiguous it should be combined with
one or more identifiers in the `specs` field.

One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s
identifying resources for installing or enabling the software named in
the `package` field. Implementations may provide resolvers which map
these software identifier IRIs to some configuration action; or they can
use only the name from the `package` field on a best effort basis.

For example, the IRI https://packages.debian.org/bowtie could
be resolved with `apt-get install bowtie`. The IRI
https://anaconda.org/bioconda/bowtie could be resolved with `conda
install -c bioconda bowtie`.

IRIs can also be system independent and used to map to a specific
software installation or selection mechanism.
Using [RRID](https://www.identifiers.org/rrid/) as an example:
https://identifiers.org/rrid/RRID:SCR_005476
could be fulfilled using the above-mentioned Debian or bioconda
package, a local installation managed by [Environment Modules](https://modules.sourceforge.net/),
or any other mechanism the platform chooses. IRIs can also be from
identifier sources that are discipline specific yet still system
independent. As an example, the equivalent [ELIXIR Tools and Data
Service Registry](https://bio.tools) IRI to the previous RRID example is
https://bio.tools/tool/bowtie2/version/2.2.8.
If supported by a given registry, implementations are encouraged to
query these system independent software identifier IRIs directly for
links to packaging systems.

A site specific IRI can be listed as well. For example, an academic
computing cluster using Environment Modules could list the IRI
`https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that
`module load bowtie-tbb/1.1.2` should be executed to make available
`bowtie` version 1.1.2 compiled with the TBB library prior to running
the accompanying Workflow or CommandLineTool. Note that the example IRI
is specific to a particular institution and computing environment as
the Environment Modules system does not have a common namespace or
standardized naming convention.

This last example is the least portable and should only be used if
mechanisms based off of the `package` field or more generic IRIs are
unavailable or unsuitable. While harmless to other sites, site specific
software IRIs should be left out of shared CWL descriptions to avoid
clutter.

The (optional) versions of the software that are known to be
compatible.

A list of software packages that should be configured in the environment of
the defined process.

Always 'SoftwareRequirement'

The list of software to be configured.

Indicate that the workflow platform must support the `valueFrom` field
of [WorkflowStepInput](#WorkflowStepInput).

Always 'StepInputExpressionRequirement'

Indicates that the workflow platform must support nested workflows in
the `run` field of [WorkflowStep](#WorkflowStep).

Always 'SubworkflowFeatureRequirement'

Set an upper limit on the execution time of a CommandLineTool.
A CommandLineTool whose execution duration exceeds the time
limit may be preemptively terminated and considered failed.
May also be used by batch systems to make scheduling decisions.
The execution duration excludes external operations, such as
staging of files, pulling a docker image etc, and only counts
wall-time for the execution of the command line itself.

Always 'ToolTimeLimit'

The time limit, in seconds.  A time limit of zero means no
time limit.  Negative time limits are an error.

For implementations that support reusing output from past work (on
the assumption that same code and same input produce same
results), control whether to enable or disable the reuse behavior
for a particular tool or step (to accommodate situations where that
assumption is incorrect).  A reused step is not executed but
instead returns the same output as the original execution.

If `WorkReuse` is not specified, correct tools should assume it
is enabled by default.

Always 'WorkReuse'

A workflow describes a set of **steps** and the **dependencies** between
those steps.  When a step produces output that will be consumed by a
second step, the first step is a dependency of the second step.

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

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

The `source` field on each workflow step input parameter expresses
the data links that contribute to the value of the step input
parameter (the "sink").  A workflow step can only begin execution
when every data link connected to a step has been fulfilled.

The `outputSource` field on each workflow step input parameter
expresses the data links that contribute to the value of the
workflow output parameter (the "sink").  Workflow execution cannot
complete successfully until every data link connected to an output
parameter has been fulfilled.

## Workflow success and failure

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

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

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

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

# Extensions

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

CWL document version. Always required at the document root. Not
required for a Process embedded inside another Process.

A documentation string for this object, or an array of strings which should be concatenated.

Declares requirements that apply to either the runtime environment or the
workflow engine that must be met in order to execute this process.  If
an implementation cannot satisfy all requirements, or a requirement is
listed which is not recognized by the implementation, it is a fatal
error and the implementation must not attempt to run the process,
unless overridden at user option.

The unique identifier for this object.

Only useful for `$graph` at `Process` level. Should not be exposed
to users in graphical or terminal user interfaces.

Specify valid types of data that may be assigned to this parameter.

A short, human-readable label of this object.

Defines the parameters representing the output of the process.  May be
used to generate and/or validate the output object.

Specify valid types of data that may be assigned to this parameter.

Declares requirements that apply to either the runtime environment or the
workflow engine that must be met in order to execute this process.  If
an implementation cannot satisfy all requirements, or a requirement is
listed which is not recognized by the implementation, it is a fatal
error and the implementation must not attempt to run the process,
unless overridden at user option.

The individual steps that make up the workflow.  Each step is executed when all of its
input data links are fulfilled.  An implementation may choose to execute
the steps in a different order than listed and/or execute steps
concurrently, provided that dependencies between steps are met.

Auto-generated class implementation for https://w3id.org/cwl/cwl#WorkflowInputParameter

The default value to use for this parameter if the parameter is missing
from the input object, or if the value of the parameter in the input
object is `null`.  Default values are applied before evaluating expressions
(e.g. dependent `valueFrom` fields).

A documentation string for this object, or an array of strings which should be concatenated.

Only valid when `type: File` or is an array of `items: File`.

This must be one or more IRIs of concept nodes
that represents file formats which are allowed as input to this
parameter, preferably defined within an ontology.  If no ontology is
available, file formats may be tested by exact match.

The unique identifier for this object.

Deprecated.  Preserved for v1.0 backwards compatibility.  Will be removed in
CWL v2.0.  Use `WorkflowInputParameter.loadContents` instead.

A short, human-readable label of this object.

Only valid when `type: File` or is an array of `items: File`.

If true, the file (or each file in the array) must be a UTF-8
text file 64 KiB or smaller, and the implementation must read
the entire contents of the file (or file array) and place it
in the `contents` field of the File object for use by
expressions.  If the size of the file is greater than 64 KiB,
the implementation must raise a fatal error.

Only valid when `type: Directory` or is an array of `items: Directory`.

Specify the desired behavior for loading the `listing` field of
a Directory object for use by expressions.

The order of precedence for loadListing is:

  1. `loadListing` on an individual parameter
  2. Inherited from `LoadListingRequirement`
  3. By default: `no_listing`

Only valid when `type: File` or is an array of `items: File`.

A value of `true` indicates that the file is read or written
sequentially without seeking.  An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe.  Default: `false`.

Specify valid types of data that may be assigned to this parameter.

Describe an output parameter of a workflow.  The parameter must be
connected to one or more parameters defined in the workflow that
will provide the value of the output parameter. It is legal to
connect a WorkflowInputParameter to a WorkflowOutputParameter.

See [WorkflowStepInput](#WorkflowStepInput) for discussion of
`linkMerge` and `pickValue`.

Only valid when `type: File` or is an array of `items: File`.

This is the file format that will be assigned to the output
File object.

The unique identifier for this object.

The method to use to merge multiple sources into a single array.
If not specified, the default method is "merge_nested".

Specifies one or more names of an output from a workflow step (in the form
`step_name/output_name` with a `/` separator`), or a workflow input name,
that supply their value(s) to the output parameter.
the output parameter.  It is valid to reference workflow level inputs
here.

The method to use to choose non-null elements among multiple sources.

A workflow step is an executable element of a workflow.  It specifies the
underlying process implementation (such as `CommandLineTool` or another
`Workflow`) in the `run` field and connects the input and output parameters
of the underlying process to workflow parameters.

# Scatter/gather

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

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

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

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

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

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

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

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

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

# Conditional execution (Optional)

Conditional execution makes execution of a step conditional on an
expression.  A step that is not executed is "skipped".  A skipped
step produces `null` for all output parameters.

The condition is evaluated after `scatter`, using the input object
of each individual scatter job.  This means over a set of scatter
jobs, some may be executed and some may be skipped.  When the
results are gathered, skipped steps must be `null` in the output
arrays.

The `when` field controls conditional execution.  This is an
expression that must be evaluated with `inputs` bound to the step
input object (or individual scatter job), and returns a boolean
value.  It is an error if this expression returns a value other
than `true` or `false`.

Conditionals in CWL are an optional feature and are not required
to be implemented by all consumers of CWL documents.  An
implementation that does not support conditionals must return a
fatal error when attempting to execute a workflow that uses
conditional constructs the implementation does not support.

# Subworkflows

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

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

Declares hints applying to either the runtime environment or the
workflow engine that may be helpful in executing this workflow step.  It is
not an error if an implementation cannot satisfy all hints, however
the implementation may report a warning.

The unique identifier for this object.

Defines the input parameters of the workflow step.  The process is ready to
run when all required input parameters are associated with concrete
values.  Input parameters include a schema for each parameter which is
used to validate the input object.  It may also be used build a user
interface for constructing the input object.

Defines the parameters representing the output of the process.  May be
used to generate and/or validate the output object.

Declares requirements that apply to either the runtime environment or the
workflow engine that must be met in order to execute this workflow step.  If
an implementation cannot satisfy all requirements, or a requirement is
listed which is not recognized by the implementation, it is a fatal
error and the implementation must not attempt to run the process,
unless overridden at user option.

Specifies the process to run.  If `run` is a string, it must be an absolute IRI
or a relative path from the primary document.

Required if `scatter` is an array of more than one element.

If defined, only run the step when the expression evaluates to
`true`.  If `false` the step is skipped.  A skipped step
produces a `null` on each output.

The input of a workflow step connects an upstream parameter (from the
workflow inputs, or the outputs of other workflows steps) with the input
parameters of the process specified by the `run` field. Only input parameters
declared by the target process will be passed through at runtime to the process
though additional parameters may be specified (for use within `valueFrom`
expressions for instance) - unconnected or unused parameters do not represent an
error condition.

# Input object

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

# Merging multiple inbound data links

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

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

If both `linkMerge` and `pickValue` are null or not specified, and
there is only a single element in the `source`, then the input
parameter takes the scalar value from the single input link (it is
*not* wrapped in a single-list).

* **merge_nested**

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

* **merge_flattened**

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

# Picking non-null values among inbound data links

If present, `pickValue` specifies how to pick non-null values among inbound data links.

`pickValue` is evaluated
  1. Once all source values from upstream step or parameters are available.
  2. After `linkMerge`.
  3. Before `scatter` or `valueFrom`.

This is specifically intended to be useful in combination with
[conditional execution](#WorkflowStep), where several upstream
steps may be connected to a single input (`source` is a list), and
skipped steps produce null values.

Static type checkers should check for type consistency after inferring what the type
will be after `pickValue` is applied, just as they do currently for `linkMerge`.

* **first_non_null**

  For the first level of a list input, pick the first non-null element.  The result is a scalar.
  It is an error if there is no non-null element.  Examples:
  * `[null, x, null, y] -> x`
  * `[null, [null], null, y] -> [null]`
  * `[null, null, null] -> Runtime Error`

  *Intended use case*: If-else pattern where the
  value comes either from a conditional step or from a default or
  fallback value. The conditional step(s) should be placed first in
  the list.

* **the_only_non_null**

  For the first level of a list input, pick the single non-null element.  The result is a scalar.
  It is an error if there is more than one non-null element.  Examples:

  * `[null, x, null] -> x`
  * `[null, x, null, y] -> Runtime Error`
  * `[null, [null], null] -> [null]`
  * `[null, null, null] -> Runtime Error`

  *Intended use case*: Switch type patterns where developer considers
  more than one active code path as a workflow error
  (possibly indicating an error in writing `when` condition expressions).

* **all_non_null**

  For the first level of a list input, pick all non-null values.
  The result is a list, which may be empty.  Examples:

  * `[null, x, null] -> [x]`
  * `[x, null, y] -> [x, y]`
  * `[null, [x], [null]] -> [[x], [null]]`
  * `[null, null, null] -> []`

  *Intended use case*: It is valid to have more than one source, but
   sources are conditional, so null sources (from skipped steps)
   should be filtered out.

The default value for this parameter to use if either there is no
`source` field, or the value produced by the `source` is `null`.  The
default must be applied prior to scattering or evaluating `valueFrom`.

The unique identifier for this object.

A short, human-readable label of this object.

The method to use to merge multiple inbound links into a single array.
If not specified, the default method is "merge_nested".

Only valid when `type: File` or is an array of `items: File`.

If true, the file (or each file in the array) must be a UTF-8
text file 64 KiB or smaller, and the implementation must read
the entire contents of the file (or file array) and place it
in the `contents` field of the File object for use by
expressions.  If the size of the file is greater than 64 KiB,
the implementation must raise a fatal error.

Only valid when `type: Directory` or is an array of `items: Directory`.

Specify the desired behavior for loading the `listing` field of
a Directory object for use by expressions.

The order of precedence for loadListing is:

  1. `loadListing` on an individual parameter
  2. Inherited from `LoadListingRequirement`
  3. By default: `no_listing`

Specifies one or more workflow parameters that will provide input to
the underlying step parameter.

To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must
be specified in the workflow or workflow step requirements.

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

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

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

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

Associate an output parameter of the underlying process with a workflow
parameter.  The workflow parameter (given in the `id` field) be may be used
as a `source` to connect with input parameters of other workflow steps, or
with an output parameter of the process.

A unique identifier for this workflow output parameter.  This is
the identifier to use in the `source` field of `WorkflowStepInput`
to connect the output value to downstream parameters.

The unique identifier for this object.

Represents an '$import' directive that should point toward another compatible CWL file to import where specified. The contents of the imported file should be relevant contextually where it is being imported

The schema validation of the CWL will not itself perform the '$import' to resolve and validate its contents. Therefore, the complete schema will not be validated entirely, and could still be partially malformed. To ensure proper and exhaustive validation of a CWL definition with this schema, all '$import' directives should be resolved and extended beforehand

Represents an '$include' directive that should point toward another compatible CWL file to import where specified. The contents of the imported file should be relevant contextually where it is being imported

The schema validation of the CWL will not itself perform the '$include' to resolve and validate its contents. Therefore, the complete schema will not be validated entirely, and could still be partially malformed. To ensure proper and exhaustive validation of a CWL definition with this schema, all '$include' directives should be resolved and extended beforehand

Metadata for a CWL document

The namespaces used in the document

The schemas used in the document

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandInputRecordField

A documentation string for this object, or an array of strings which should be concatenated.

Only valid when `type: File` or is an array of `items: File`.

This must be one or more IRIs of concept nodes
that represents file formats which are allowed as input to this
parameter, preferably defined within an ontology.  If no ontology is
available, file formats may be tested by exact match.

Describes how to turn this object into command line arguments.

The name of the field

Only valid when `type: File` or is an array of `items: File`.

A value of `true` indicates that the file is read or written
sequentially without seeking.  An implementation may use this flag to
indicate whether it is valid to stream file contents using a named
pipe.  Default: `false`.

The field type

The field type

Auto-generated class implementation for https://w3id.org/cwl/cwl#InputRecordField

The name of the field

The field type

The field type

Auto-generated class implementation for https://w3id.org/cwl/cwl#CommandOutputRecordField

Only valid when `type: File` or is an array of `items: File`.

This is the file format that will be assigned to the output
File object.

A short, human-readable label of this object.

The name of the field

Describes how to generate this output object based on the files
produced by a CommandLineTool

The field type

The field type

Auto-generated class implementation for https://w3id.org/cwl/cwl#OutputRecordField

The name of the field

The field type

The field type

Additional code fragments that will also be inserted
before executing the expression code.  Allows for function definitions that may
be called from CWL expressions.

Indicates that the workflow platform must support inline Javascript expressions.
If this requirement is not present, the workflow platform must not perform expression
interpolation.

The list of type definitions.

Specify the desired behavior for loading the `listing` field of
a Directory object for use by expressions.

Supply the contents of a Dockerfile which will be built using `docker build`.

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.

Provide HTTP URL to download and gunzip a Docker images using `docker import.

Specify an HTTP URL from which to download a Docker image using `docker load`.

Set the designated output directory to a specific location inside the
Docker container.

Specify a Docker image to retrieve using `docker pull`. Can contain the
immutable digest to ensure an exact container is used:
`dockerPull: ubuntu@sha256:45b23dee08af5e43a7fea6c4cf9c25ccf269ee113168c19722f87876677c5cb2`

The list of software to be configured.

A list of software packages that should be configured in the environment of
the defined process.

The list of environment variables.

Define a list of environment variables which will be set in the
execution environment of the tool.  See `EnvironmentDef` for details.

Maximum reserved number of CPU cores.

See `coresMin` for discussion about fractional CPU requests.

Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)

See `outdirMin` for discussion about fractional storage requests.

Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) (default is 1024)

May be a fractional value.  If so, the actual storage request
must be rounded up to the next whole number.  The reported
amount of storage reserved for the process, which is available
to expressions on the CommandLineTool as `runtime.outdirSize`,
must be a non-zero integer.

Maximum reserved RAM in mebibytes (2**20)

See `ramMin` for discussion about fractional RAM requests.

Minimum reserved RAM in mebibytes (2**20) (default is 256)

May be a fractional value.  If so, the actual RAM request must
be rounded up to the next whole number.  The reported amount of
RAM reserved for the process, which is available to
expressions on the CommandLineTool as `runtime.ram`, must be a
non-zero integer.

Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)

See `tmpdirMin` for discussion about fractional storage requests.

Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) (default is 1024)

May be a fractional value.  If so, the actual storage request
must be rounded up to the next whole number.  The reported
amount of storage reserved for the process, which is available
to expressions on the CommandLineTool as `runtime.tmpdirSize`,
must be a non-zero integer.

The time limit, in seconds.  A time limit of zero means no
time limit.  Negative time limits are an error.

Set an upper limit on the execution time of a CommandLineTool.
A CommandLineTool whose execution duration exceeds the time
limit may be preemptively terminated and considered failed.
May also be used by batch systems to make scheduling decisions.
The execution duration excludes external operations, such as
staging of files, pulling a docker image etc, and only counts
wall-time for the execution of the command line itself.

Indicates that the workflow platform must support nested workflows in
the `run` field of [WorkflowStep](#WorkflowStep).

Indicates that the workflow platform must support the `scatter` and
`scatterMethod` fields of [WorkflowStep](#WorkflowStep).

Indicates that the workflow platform must support multiple inbound data links
listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput).

Indicate that the workflow platform must support the `valueFrom` field
of [WorkflowStepInput](#WorkflowStepInput).

CWL document version. Always required at the document root. Not
required for a Process embedded inside another Process.

Provide a JSON object that satisfies the schema "cwl_schema". Here are the required top‑level fields: none (all optional). Return only the valid JSON object.