--- a/env/lib/python3.7/site-packages/cwltool/schemas/v1.0/CommandLineTool.yml	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,966 +0,0 @@
-$base: "https://w3id.org/cwl/cwl#"
-
-$namespaces:
-  cwl: "https://w3id.org/cwl/cwl#"
-
-$graph:
-
-- name: CommandLineToolDoc
-  type: documentation
-  doc:
-    - |
-      # Common Workflow Language (CWL) Command Line Tool Description, v1.0.2
-
-      This version:
-        * https://w3id.org/cwl/v1.0/
-
-      Current version:
-        * https://w3id.org/cwl/
-    - "\n\n"
-    - {$include: contrib.md}
-    - "\n\n"
-    - |
-      # Abstract
-
-      A Command Line Tool is a non-interactive executable program that reads
-      some input, performs a computation, and terminates after producing some
-      output.  Command line programs are a flexible unit of code sharing and
-      reuse, unfortunately the syntax and input/output semantics among command
-      line programs is extremely heterogeneous. A common layer for describing
-      the syntax and semantics of programs can reduce this incidental
-      complexity by providing a consistent way to connect programs together.
-      This specification defines the Common Workflow Language (CWL) Command
-      Line Tool Description, a vendor-neutral standard for describing the
-      syntax and input/output semantics of command line programs.
-
-    - {$include: intro.md}
-
-    - |
-      ## Introduction to CWL Command Line Tool standard v1.0.2
-
-      This specification represents the third stable release from the CWL
-      group.  Since the initial v1.0 release, v1.0.2 introduces the following
-      updates to the CWL Command Line Tool standard.  Documents should continue
-      to use `cwlVersion: v1.0` and existing v1.0 documents remain valid,
-      however CWL documents that relied on previously undefined or
-      underspecified behavior may have slightly different behavior in v1.0.2.
-
-        * 13 July 2016: Mark `baseCommand` as optional and update descriptive text.
-        * 14 November 2016: Clarify [SoftwareRequirement](#SoftwareRequirement)
-          `spec` fields.
-        * 12 March 2017:
-          * Mark `default` as not required for link checking.
-          * Add note that files in InitialWorkDir must have path in output directory.
-          * Add note that writable: true applies recursively.
-        * 23 July 2017: (v1.0.1)
-          * Add clarification about scattering over empty arrays.
-          * Clarify interpretation of `secondaryFiles` on inputs.
-          * Expanded discussion of semantics of `File` and `Directory` types
-          * Fixed typo "EMACScript" to "ECMAScript"
-          * Clarified application of input parameter default values when the input is `null` or undefined.
-          * Clarified valid types and meaning of the format field on inputs versus outputs
-          * Clarify that command line arguments must not interpreted as shell except when shellQuote: false
-          * Clarify behavior of `entryname`
-        * 10 August 2017: (v1.0.2)
-          * Clarify behavior resolving expressions in `secondaryFile`
-
-      Since draft-3, v1.0 introduces the following changes and additions
-      to the CWL Command Line Tool standard:
-
-        * The [Directory](#Directory) type.
-        * Syntax simplifcations: denoted by the `map<>` syntax. Example: inputs
-          contains a list of items, each with an id. Now one can specify
-          a mapping of that identifier to the corresponding
-          `CommandInputParamater`.
-          ```
-          inputs:
-           - id: one
-             type: string
-             doc: First input parameter
-           - id: two
-             type: int
-             doc: Second input parameter
-          ```
-          can be
-          ```
-          inputs:
-           one:
-            type: string
-            doc: First input parameter
-           two:
-            type: int
-            doc: Second input parameter
-          ```
-        * [InitialWorkDirRequirement](#InitialWorkDirRequirement): list of
-          files and subdirectories to be present in the output directory prior
-          to execution.
-        * Shortcuts for specifying the standard [output](#stdout) and/or
-          [error](#stderr) streams as a (streamable) File output.
-        * [SoftwareRequirement](#SoftwareRequirement) for describing software
-          dependencies of a tool.
-        * The common `description` field has been renamed to `doc`.
-
-
-      ## Purpose
-
-      Standalone programs are a flexible and interoperable form of code reuse.
-      Unlike monolithic applications, applications and analysis workflows which
-      are composed of multiple separate programs can be written in multiple
-      languages and execute concurrently on multiple hosts.  However, POSIX
-      does not dictate computer-readable grammar or semantics for program input
-      and output, resulting in extremely heterogeneous command line grammar and
-      input/output semantics among program.  This is a particular problem in
-      distributed computing (multi-node compute clusters) and virtualized
-      environments (such as Docker containers) where it is often necessary to
-      provision resources such as input files before executing the program.
-
-      Often this gap is filled by hard coding program invocation and
-      implicitly assuming requirements will be met, or abstracting program
-      invocation with wrapper scripts or descriptor documents.  Unfortunately,
-      where these approaches are application or platform specific it creates a
-      significant barrier to reproducibility and portability, as methods
-      developed for one platform must be manually ported to be used on new
-      platforms.  Similarly it creates redundant work, as wrappers for popular
-      tools must be rewritten for each application or platform in use.
-
-      The Common Workflow Language Command Line Tool Description is designed to
-      provide a common standard description of grammar and semantics for
-      invoking programs used in data-intensive fields such as Bioinformatics,
-      Chemistry, Physics, Astronomy, and Statistics.  This specification
-      defines a precise data and execution model for Command Line Tools that
-      can be implemented on a variety of computing platforms, ranging from a
-      single workstation to cluster, grid, cloud, and high performance
-      computing platforms.
-
-    - {$include: concepts.md}
-    - {$include: invocation.md}
-
-
-- type: record
-  name: EnvironmentDef
-  doc: |
-    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.
-  fields:
-    - name: envName
-      type: string
-      doc: The environment variable name
-    - name: envValue
-      type: [string, Expression]
-      doc: The environment variable value
-
-- type: record
-  name: CommandLineBinding
-  extends: InputBinding
-  doc: |
-
-    When listed under `inputBinding` in the input schema, the term
-    "value" refers to the 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.
-
-      - **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.
-
-      - **object**: Add `prefix` only, and recursively add object fields for
-          which `inputBinding` is specified.
-
-      - **null**: Add nothing.
-
-  fields:
-    - name: position
-      type: int?
-      doc: "The sorting key.  Default position is 0."
-    - name: prefix
-      type: string?
-      doc: "Command line prefix to add before the value."
-    - name: separate
-      type: boolean?
-      doc: |
-        If true (default), then the prefix and value must be added as separate
-        command line arguments; if false, prefix and value must be concatenated
-        into a single command line argument.
-    - name: itemSeparator
-      type: string?
-      doc: |
-        Join the array elements into a single string with the elements
-        separated by by `itemSeparator`.
-    - name: valueFrom
-      type:
-        - "null"
-        - string
-        - Expression
-      jsonldPredicate: "cwl:valueFrom"
-      doc: |
-        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.
-
-        When a binding is part of the `CommandLineTool.arguments` field,
-        the `valueFrom` field is required.
-
-    - name: shellQuote
-      type: boolean?
-      doc: |
-        If `ShellCommandRequirement` is in the requirements for the current command,
-        this controls whether the value is quoted on the command line (default is true).
-        Use `shellQuote: false` to inject metacharacters for operations such as pipes.
-
-        If `shellQuote` is true or not provided, the implementation must not
-        permit interpretation of any shell metacharacters or directives.
-
-- type: record
-  name: CommandOutputBinding
-  extends: OutputBinding
-  doc: |
-    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
-  fields:
-    - name: glob
-      type:
-        - "null"
-        - string
-        - Expression
-        - type: array
-          items: string
-      doc: |
-        Find files relative to the output directory, using POSIX glob(3)
-        pathname matching.  If an array is provided, find files 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 which
-        actually exist.
-    - name: loadContents
-      type:
-        - "null"
-        - boolean
-      jsonldPredicate: "cwl:loadContents"
-      doc: |
-        For each file matched in `glob`, read up to
-        the first 64 KiB of text from the file and place it in the `contents`
-        field of the file object for manipulation by `outputEval`.
-    - name: outputEval
-      type:
-        - "null"
-        - string
-        - Expression
-      doc: |
-        Evaluate an expression to generate the output value.  If `glob` was
-        specified, the value of `self` must be an array containing file objects
-        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.  Additionally, if `loadContents` is `true`,
-        the File objects must include up to the first 64 KiB of file contents
-        in the `contents` field.
-
-
-- name: CommandInputRecordField
-  type: record
-  extends: InputRecordField
-  specialize:
-    - specializeFrom: InputRecordSchema
-      specializeTo: CommandInputRecordSchema
-    - specializeFrom: InputEnumSchema
-      specializeTo: CommandInputEnumSchema
-    - specializeFrom: InputArraySchema
-      specializeTo: CommandInputArraySchema
-    - specializeFrom: InputBinding
-      specializeTo: CommandLineBinding
-
-
-- name: CommandInputRecordSchema
-  type: record
-  extends: InputRecordSchema
-  specialize:
-    - specializeFrom: InputRecordField
-      specializeTo: CommandInputRecordField
-
-
-- name: CommandInputEnumSchema
-  type: record
-  extends: InputEnumSchema
-  specialize:
-    - specializeFrom: InputBinding
-      specializeTo: CommandLineBinding
-
-
-- name: CommandInputArraySchema
-  type: record
-  extends: InputArraySchema
-  specialize:
-    - specializeFrom: InputRecordSchema
-      specializeTo: CommandInputRecordSchema
-    - specializeFrom: InputEnumSchema
-      specializeTo: CommandInputEnumSchema
-    - specializeFrom: InputArraySchema
-      specializeTo: CommandInputArraySchema
-    - specializeFrom: InputBinding
-      specializeTo: CommandLineBinding
-
-
-- name: CommandOutputRecordField
-  type: record
-  extends: OutputRecordField
-  specialize:
-    - specializeFrom: OutputRecordSchema
-      specializeTo: CommandOutputRecordSchema
-    - specializeFrom: OutputEnumSchema
-      specializeTo: CommandOutputEnumSchema
-    - specializeFrom: OutputArraySchema
-      specializeTo: CommandOutputArraySchema
-    - specializeFrom: OutputBinding
-      specializeTo: CommandOutputBinding
-
-
-- name: CommandOutputRecordSchema
-  type: record
-  extends: OutputRecordSchema
-  specialize:
-    - specializeFrom: OutputRecordField
-      specializeTo: CommandOutputRecordField
-
-
-- name: CommandOutputEnumSchema
-  type: record
-  extends: OutputEnumSchema
-  specialize:
-    - specializeFrom: OutputRecordSchema
-      specializeTo: CommandOutputRecordSchema
-    - specializeFrom: OutputEnumSchema
-      specializeTo: CommandOutputEnumSchema
-    - specializeFrom: OutputArraySchema
-      specializeTo: CommandOutputArraySchema
-    - specializeFrom: OutputBinding
-      specializeTo: CommandOutputBinding
-
-
-- name: CommandOutputArraySchema
-  type: record
-  extends: OutputArraySchema
-  specialize:
-    - specializeFrom: OutputRecordSchema
-      specializeTo: CommandOutputRecordSchema
-    - specializeFrom: OutputEnumSchema
-      specializeTo: CommandOutputEnumSchema
-    - specializeFrom: OutputArraySchema
-      specializeTo: CommandOutputArraySchema
-    - specializeFrom: OutputBinding
-      specializeTo: CommandOutputBinding
-
-
-- type: record
-  name: CommandInputParameter
-  extends: InputParameter
-  doc: An input parameter for a CommandLineTool.
-  specialize:
-    - specializeFrom: InputRecordSchema
-      specializeTo: CommandInputRecordSchema
-    - specializeFrom: InputEnumSchema
-      specializeTo: CommandInputEnumSchema
-    - specializeFrom: InputArraySchema
-      specializeTo: CommandInputArraySchema
-    - specializeFrom: InputBinding
-      specializeTo: CommandLineBinding
-
-- type: record
-  name: CommandOutputParameter
-  extends: OutputParameter
-  doc: An output parameter for a CommandLineTool.
-  specialize:
-    - specializeFrom: OutputBinding
-      specializeTo: CommandOutputBinding
-  fields:
-    - name: type
-      type:
-        - "null"
-        - CWLType
-        - stdout
-        - stderr
-        - CommandOutputRecordSchema
-        - CommandOutputEnumSchema
-        - CommandOutputArraySchema
-        - string
-        - type: array
-          items:
-            - CWLType
-            - CommandOutputRecordSchema
-            - CommandOutputEnumSchema
-            - CommandOutputArraySchema
-            - string
-      jsonldPredicate:
-        "_id": "sld:type"
-        "_type": "@vocab"
-        refScope: 2
-        typeDSL: True
-      doc: |
-        Specify valid types of data that may be assigned to this parameter.
-
-- name: stdout
-  type: enum
-  symbols: [ "cwl:stdout" ]
-  docParent: "#CommandOutputParameter"
-  doc: |
-    Only valid as a `type` for a `CommandLineTool` output with no
-    `outputBinding` set.
-
-    The following
-    ```
-    outputs:
-      an_output_name:
-        type: stdout
-
-    stdout: a_stdout_file
-    ```
-    is equivalent to
-    ```
-    outputs:
-      an_output_name:
-        type: File
-        streamable: true
-        outputBinding:
-          glob: a_stdout_file
-
-    stdout: a_stdout_file
-    ```
-
-    If there is no `stdout` name provided, a random filename will be created.
-    For example, the following
-    ```
-    outputs:
-      an_output_name:
-        type: stdout
-    ```
-    is equivalent to
-    ```
-    outputs:
-      an_output_name:
-        type: File
-        streamable: true
-        outputBinding:
-          glob: random_stdout_filenameABCDEFG
-
-    stdout: random_stdout_filenameABCDEFG
-    ```
-
-
-- name: stderr
-  type: enum
-  symbols: [ "cwl:stderr" ]
-  docParent: "#CommandOutputParameter"
-  doc: |
-    Only valid as a `type` for a `CommandLineTool` output with no
-    `outputBinding` set.
-
-    The following
-    ```
-    outputs:
-      an_output_name:
-      type: stderr
-
-    stderr: a_stderr_file
-    ```
-    is equivalent to
-    ```
-    outputs:
-      an_output_name:
-        type: File
-        streamable: true
-        outputBinding:
-          glob: a_stderr_file
-
-    stderr: a_stderr_file
-    ```
-
-    If there is no `stderr` name provided, a random filename will be created.
-    For example, the following
-    ```
-    outputs:
-      an_output_name:
-        type: stderr
-    ```
-    is equivalent to
-    ```
-    outputs:
-      an_output_name:
-        type: File
-        streamable: true
-        outputBinding:
-          glob: random_stderr_filenameABCDEFG
-
-    stderr: random_stderr_filenameABCDEFG
-    ```
-
-
-- type: record
-  name: CommandLineTool
-  extends: Process
-  documentRoot: true
-  specialize:
-    - specializeFrom: InputParameter
-      specializeTo: CommandInputParameter
-    - specializeFrom: OutputParameter
-      specializeTo: CommandOutputParameter
-  doc: |
-    This defines the schema of the CWL Command Line Tool Description document.
-
-  fields:
-    - name: class
-      jsonldPredicate:
-        "_id": "@type"
-        "_type": "@vocab"
-      type: string
-    - name: baseCommand
-      doc: |
-        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.
-      type:
-        - string?
-        - string[]?
-      jsonldPredicate:
-        "_id": "cwl:baseCommand"
-        "_container": "@list"
-    - name: arguments
-      doc: |
-        Command line bindings which are not directly associated with input parameters.
-      type:
-        - "null"
-        - type: array
-          items: [string, Expression, CommandLineBinding]
-      jsonldPredicate:
-        "_id": "cwl:arguments"
-        "_container": "@list"
-    - name: stdin
-      type: ["null", string, Expression]
-      doc: |
-        A path to a file whose contents must be piped into the command's
-        standard input stream.
-    - name: stderr
-      type: ["null", string, Expression]
-      jsonldPredicate: "https://w3id.org/cwl/cwl#stderr"
-      doc: |
-        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.
-    - name: stdout
-      type: ["null", string, Expression]
-      jsonldPredicate: "https://w3id.org/cwl/cwl#stdout"
-      doc: |
-        Capture the command's standard output stream to a file written to
-        the designated output directory.
-
-        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.
-    - name: successCodes
-      type: int[]?
-      doc: |
-        Exit codes that indicate the process completed successfully.
-
-    - name: temporaryFailCodes
-      type: int[]?
-      doc: |
-        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.
-
-    - name: permanentFailCodes
-      type: int[]?
-      doc:
-        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.
-
-
-- type: record
-  name: DockerRequirement
-  extends: ProcessRequirement
-  doc: |
-    Indicates that a workflow component should be run in a
-    [Docker](http://docker.com) container, and specifies how to fetch or build
-    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 may rewrite
-    file paths in the input object to correspond to the Docker bind mounted
-    locations.
-
-    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.
-
-    ## 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.
-
-  fields:
-    - name: class
-      type: string
-      doc: "Always 'DockerRequirement'"
-      jsonldPredicate:
-        "_id": "@type"
-        "_type": "@vocab"
-    - name: dockerPull
-      type: string?
-      doc: "Specify a Docker image to retrieve using `docker pull`."
-    - name: dockerLoad
-      type: string?
-      doc: "Specify a HTTP URL from which to download a Docker image using `docker load`."
-    - name: dockerFile
-      type: string?
-      doc: "Supply the contents of a Dockerfile which will be built using `docker build`."
-    - name: dockerImport
-      type: string?
-      doc: "Provide HTTP URL to download and gunzip a Docker images using `docker import."
-    - name: dockerImageId
-      type: string?
-      doc: |
-        The image id that will be used for `docker run`.  May be a
-        human-readable image name or the image identifier hash.  May be skipped
-        if `dockerPull` is specified, in which case the `dockerPull` image id
-        must be used.
-    - name: dockerOutputDirectory
-      type: string?
-      doc: |
-        Set the designated output directory to a specific location inside the
-        Docker container.
-
-
-- type: record
-  name: SoftwareRequirement
-  extends: ProcessRequirement
-  doc: |
-    A list of software packages that should be configured in the environment of
-    the defined process.
-  fields:
-    - name: class
-      type: string
-      doc: "Always 'SoftwareRequirement'"
-      jsonldPredicate:
-        "_id": "@type"
-        "_type": "@vocab"
-    - name: packages
-      type: SoftwarePackage[]
-      doc: "The list of software to be configured."
-      jsonldPredicate:
-        mapSubject: package
-        mapPredicate: specs
-
-- name: SoftwarePackage
-  type: record
-  fields:
-    - name: package
-      type: string
-      doc: |
-        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.
-    - name: version
-      type: string[]?
-      doc: |
-        The (optional) versions of the software that are known to be
-        compatible.
-    - name: specs
-      type: string[]?
-      doc: |
-        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 identifer 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 [Environement Modules](http://modules.sourceforge.net/),
-        or any other mechanism the platform chooses. IRIs can also be from
-        identifer 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 sofware identifier IRIs directly for
-        links to packaging systems.
-
-        A site specific IRI can be listed as well. For example, an academic
-        computing cluster using Environement 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.
-
-- name: Dirent
-  type: record
-  doc: |
-    Define a file or subdirectory that must be placed in the designated output
-    directory prior to executing the command line tool.  May be the result of
-    executing an expression, such as building a configuration file from a
-    template.
-  fields:
-    - name: entryname
-      type: ["null", string, Expression]
-      jsonldPredicate:
-        _id: cwl:entryname
-      doc: |
-        The name of the file or subdirectory to create in the output directory.
-        If `entry` is a File or Directory, the `entryname` field overrides the value
-        of `basename` of the File or Directory object.  Optional.
-    - name: entry
-      type: [string, Expression]
-      jsonldPredicate:
-        _id: cwl:entry
-      doc: |
-        If the value is a string literal or an expression which evaluates to a
-        string, a new file must be created with the string as the file contents.
-
-        If the value is an expression that evaluates to a `File` object, this
-        indicates the referenced file should be added to the designated output
-        directory prior to executing the tool.
-
-        If the value is an expression that evaluates to a `Dirent` object, this
-        indicates that the File or Directory in `entry` should be added to the
-        designated output directory with the name in `entryname`.
-
-        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.
-    - name: writable
-      type: boolean?
-      doc: |
-        If true, the file or directory 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.  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.
-
-
-- name: InitialWorkDirRequirement
-  type: record
-  extends: ProcessRequirement
-  doc:
-    Define a list of files and subdirectories that must be created by the
-    workflow platform in the designated output directory prior to executing the
-    command line tool.
-  fields:
-    - name: class
-      type: string
-      doc: InitialWorkDirRequirement
-      jsonldPredicate:
-        "_id": "@type"
-        "_type": "@vocab"
-    - name: listing
-      type:
-        - type: array
-          items: [File, Directory, Dirent, string, Expression]
-        - string
-        - Expression
-      jsonldPredicate:
-        _id: "cwl:listing"
-      doc: |
-        The list of files or subdirectories that must be placed in the
-        designated output directory prior to executing the command line tool.
-
-        May be an expression.  If so, the expression return value must validate
-        as `{type: array, items: [File, Directory]}`.
-
-        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 in the designated output directory.
-        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.
-
-
-- name: EnvVarRequirement
-  type: record
-  extends: ProcessRequirement
-  doc: |
-    Define a list of environment variables which will be set in the
-    execution environment of the tool.  See `EnvironmentDef` for details.
-  fields:
-    - name: class
-      type: string
-      doc: "Always 'EnvVarRequirement'"
-      jsonldPredicate:
-        "_id": "@type"
-        "_type": "@vocab"
-    - name: envDef
-      type: EnvironmentDef[]
-      doc: The list of environment variables.
-      jsonldPredicate:
-        mapSubject: envName
-        mapPredicate: envValue
-
-
-- type: record
-  name: ShellCommandRequirement
-  extends: ProcessRequirement
-  doc: |
-    Modify the behavior of CommandLineTool to generate a single string
-    containing a shell command line.  Each item in the argument list must be
-    joined into a string separated by single spaces and quoted to prevent
-    intepretation 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.
-  fields:
-    - name: class
-      type: string
-      doc: "Always 'ShellCommandRequirement'"
-      jsonldPredicate:
-        "_id": "@type"
-        "_type": "@vocab"
-
-
-- type: record
-  name: ResourceRequirement
-  extends: ProcessRequirement
-  doc: |
-    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 permitted
-    to use. 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 "max" resource allocation, an
-    implementation may deny additional resources, which may result in job
-    failure.
-
-    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, an implementation may provide a default.
-
-  fields:
-    - name: class
-      type: string
-      doc: "Always 'ResourceRequirement'"
-      jsonldPredicate:
-        "_id": "@type"
-        "_type": "@vocab"
-    - name: coresMin
-      type: ["null", long, string, Expression]
-      doc: Minimum reserved number of CPU cores
-
-    - name: coresMax
-      type: ["null", int, string, Expression]
-      doc: Maximum reserved number of CPU cores
-
-    - name: ramMin
-      type: ["null", long, string, Expression]
-      doc: Minimum reserved RAM in mebibytes (2**20)
-
-    - name: ramMax
-      type: ["null", long, string, Expression]
-      doc: Maximum reserved RAM in mebibytes (2**20)
-
-    - name: tmpdirMin
-      type: ["null", long, string, Expression]
-      doc: Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
-
-    - name: tmpdirMax
-      type: ["null", long, string, Expression]
-      doc: Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
-
-    - name: outdirMin
-      type: ["null", long, string, Expression]
-      doc: Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
-
-    - name: outdirMax
-      type: ["null", long, string, Expression]
-      doc: Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)