Defines the type of the array elements.

Must be array

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

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 to the command line.

• Directory: Add prefix and the value of Directory.path 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.

A short, human-readable label of this object.

The identifier for this type

Defines the set of valid symbols.

Must be enum

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

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 to the command line.

• Directory: Add prefix and the value of Directory.path 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.

A short, human-readable label of this object.

The identifier for this type

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

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.

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 to the command line.

• Directory: Add prefix and the value of Directory.path 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.

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.

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.

Must be record

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

Defines the fields of the 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 to the command line.

• Directory: Add prefix and the value of Directory.path 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.

A short, human-readable label of this object.

The identifier for this type

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 or CWL Expression 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.

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.

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

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.

An identifier for the type of computational operation, of this Process. Especially useful for Operation, but can also be used for CommandLineTool, Workflow, or 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, like Alignment, or Clustering; or a more specific Operation concept like Split read mapping.

A short, human-readable label of this object.

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.

Defines the type of the array elements.

Must be array

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

A short, human-readable label of this object.

The identifier for this type

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.

Defines the set of valid symbols.

Must be enum

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

A short, human-readable label of this object.

The identifier for this type

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

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.

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

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.

Must be record

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 Directory to indicate this object describes a Directory.

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.

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 (|,&, ;, <, >, (,), $,`, \, ", ', <space>, <tab>, and <newline>) or characters not allowed for Internationalized Domain Names for Applications then implementations may terminate the process with a permanentFailure.

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.

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.

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

Always 'EnvVarRequirement'

The list of environment variables.

The environment variable name

The environment variable value

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

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.

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

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.

An identifier for the type of computational operation, of this Process. Especially useful for Operation, but can also be used for CommandLineTool, Workflow, or 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, like Alignment, or Clustering; or a more specific Operation concept like Split read mapping.

A short, human-readable label of this object.

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.

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.

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.

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.

Must be File to indicate this object describes a file.

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.

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 (|,&, ;, <, >, (,), $,`, \, ", ', <space>, <tab>, and <newline>) or characters not allowed for Internationalized Domain Names for Applications 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)

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.

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.

Always 'InplaceUpdateRequirement'

Defines the type of the array elements.

Must be array

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

A short, human-readable label of this object.

The identifier for this type

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

Defines the set of valid symbols.

Must be enum

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

A short, human-readable label of this object.

The identifier for this type

Must be record

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

Always 'LoadListingRequirement'

Always 'MultipleInputFeatureRequirement'

Always 'NetworkAccess'

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.

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

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.

An identifier for the type of computational operation, of this Process. Especially useful for Operation, but can also be used for CommandLineTool, Workflow, or 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, like Alignment, or Clustering; or a more specific Operation concept like Split read mapping.

A short, human-readable label of this object.

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.

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

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.

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.

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.

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.

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.

Defines the type of the array elements.

Must be array

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

A short, human-readable label of this object.

The identifier for this type

Defines the set of valid symbols.

Must be enum

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

A short, human-readable label of this object.

The identifier for this type

Must be record

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

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.

Always 'ScatterFeatureRequirement'

Always 'SchemaDefRequirement'

The list of type definitions.

Always 'ShellCommandRequirement'

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 IRIs 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 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, 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 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.

Always 'SoftwareRequirement'

The list of software to be configured.

Always 'StepInputExpressionRequirement'

Always 'SubworkflowFeatureRequirement'

Always 'ToolTimeLimit'

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

Always 'WorkReuse'

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.

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

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.

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.

An identifier for the type of computational operation, of this Process. Especially useful for Operation, but can also be used for CommandLineTool, Workflow, or 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, like Alignment, or Clustering; or a more specific Operation concept like Split read mapping.

A short, human-readable label of this object.

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.

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

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.

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

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.

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.

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.

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.

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.

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.

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

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

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.

A short, human-readable label of this 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.

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 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

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

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

To use valueFrom, 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.

The unique identifier for this object.

The namespaces used in the document

The schemas used in the document

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

The list of type definitions.

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.

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.

The list of environment variables.

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.

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

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