Language cleanup

.github/config/wordlist.txt

@@ -122,6 +122,7 @@ implementer
 implementers
 implementor
 implementors
+initialworkdir
 initialworkdirrequirement
 initialworkdirrequirements
 inlinejavascriptrequirement

CommandLineTool.yml

@@ -52,6 +52,20 @@ $graph:
       ## Changelog for v1.3.0-dev1
 
       See also the [CWL Workflow Description, v1.3.0-dev1 changelog](Workflow.html#Changelog).
+
+      * New field `networkAccess` on
+        [CommandLineTool](#CommandLineTool).  This supersedes the
+        [NetworkAccess](#NetworkAccess) requirement, which is now
+        deprecated.
+      * New field `envDef` on [CommandLineTool](#CommandLineTool).
+        This supersedes the [EnvVarRequirement](#EnvVarRequirement)
+        requirement, which is now deprecated.
+      * New field `initialWorkDir` on
+        [CommandLineTool](#CommandLineTool).  This supersedes the
+        [InitialWorkDirRequirement](#InitialWorkDirRequirement)
+        requirement, which is now deprecated.
+
+
       For other changes since CWL v1.0, see the
       [CWL Command Line Tool Description, v1.1 changelog](https://www.commonwl.org/v1.1/CommandLineTool.html#Changelog)
       and
@@ -711,6 +725,94 @@ $graph:
 
         If not specified, all exit codes except 0 are considered permanent failure.
 
+    - name: networkAccess
+      type: ['null', boolean, Expression]
+      jsonldPredicate: "cwl:NetworkAccess/networkAccess"
+      doc: |
+        Indicate whether a process requires outgoing IPv4/IPv6 network
+        access.  Choice of IPv4 or IPv6 is implementation and site
+        specific, correct tools must support both.
+
+        If `networkAccess` is false or not specified, tools must not
+        assume network access, except for localhost (the loopback device).
+
+        If `networkAccess` is true, the tool must be able to make outgoing
+        connections to network resources.  Resources may be on a private
+        subnet or the public Internet.  However, implementations and sites
+        may apply their own security policies to restrict what is
+        accessible by the tool.
+
+        Enabling network access does not imply a publicly routable IP
+        address or the ability to accept inbound connections.
+
+    - name: initialWorkDir
+      type:
+        - 'null'
+        - Expression
+        - type: array
+          items:
+            - "null"
+            - Dirent
+            - Expression
+            - File
+            - Directory
+            - type: array
+              items:
+                - File
+                - Directory
+      doc: |
+        Define a list of files and subdirectories that must be staged
+        by the workflow platform prior to executing the command line
+        tool.  Normally this is the designated output directory, but
+        when containers are used, it is possible to stage to other
+        locations, see discussion below.
+
+        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 `initialWorkDir` must have their `path` set to
+        their staged location.  If the same File or Directory appears
+        more than once in the `initialWorkDir`, the implementation
+        must choose exactly one value for `path`; how this value is
+        chosen is undefined.
+
+        Normally files are staged within the designated output
+        directory.  However, when running inside containers, files may
+        be staged at arbitrary locations, see discussion for
+        [`Dirent.entryname`](#Dirent).  Together with
+        `DockerRequirement.dockerOutputDirectory` it is possible to
+        control the locations of both input and output files when
+        running in containers.
+
+        Files listed in `inputs` that are not listed in
+        `initialWorkDir` shall be staged to an arbitrary location on
+        the file system.  This location must be outside the designated
+        output directory.
+
+    - name: envDef
+      type: EnvironmentDef[]?
+      doc: |
+        Define a list of environment variables which will be set in
+        the execution environment of the tool.  See
+        [EnvironmentDef](#EnvironmentDef) for details.
+      jsonldPredicate:
+        "_id": "cwl:EnvVarRequirement/envDef"
+        mapSubject: envName
+        mapPredicate: envValue
+
+
 
 - type: record
   name: DockerRequirement
@@ -991,7 +1093,9 @@ $graph:
 - name: InitialWorkDirRequirement
   type: record
   extends: ProcessRequirement
-  doc:
+  doc: |
+    **Deprecated as of v1.3**  Prefer [CommandLineTool.initialWorkDir](#CommandLineTool)
+
     Define a list of files and subdirectories that must be staged by
     the workflow platform prior to executing the command line tool.
 
@@ -1059,6 +1163,8 @@ $graph:
   type: record
   extends: ProcessRequirement
   doc: |
+    **Deprecated as of v1.3**  Prefer [CommandLineTool.envDef](#CommandLineTool)
+
     Define a list of environment variables which will be set in the
     execution environment of the tool.  See `EnvironmentDef` for details.
   fields:
@@ -1076,6 +1182,7 @@ $graph:
       type: EnvironmentDef[]
       doc: The list of environment variables.
       jsonldPredicate:
+        "_id": "cwl:EnvVarRequirement/envDef"
         mapSubject: envName
         mapPredicate: envValue
 
@@ -1291,6 +1398,8 @@ $graph:
   name: NetworkAccess
   extends: ProcessRequirement
   doc: |
+    **Deprecated as of v1.3**  Prefer [CommandLineTool.networkAccess](#CommandLineTool)
+
     Indicate whether a process requires outgoing IPv4/IPv6 network
     access.  Choice of IPv4 or IPv6 is implementation and site
     specific, correct tools must support both.
@@ -1320,6 +1429,7 @@ $graph:
         "_type": "@vocab"
     - name: networkAccess
       type: [boolean, Expression]
+      jsonldPredicate: "cwl:NetworkAccess/networkAccess"
 
 - name: InplaceUpdateRequirement
   type: record

Workflow.yml

@@ -47,6 +47,17 @@ $graph:
         feature to manage loop output data history.
 
       See also the [CWL Command Line Tool Description, v1.3.0-dev1 changelog](CommandLineTool.html#Changelog).
+
+      * Workflow steps may now specify iterative execution.  See
+        [LoopWorkflowStep](#LoopWorkflowStep)
+      * Including
+        [StepInputExpressionRequirement](#StepInputExpressionRequirement),
+        [MultipleInputFeatureRequirement](#MultipleInputFeatureRequirement),
+        [ScatterFeatureRequirement](#ScatterFeatureRequirement) and
+        [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement)
+        in `requirements` is no longer necessary to use the associated
+        feature.  These core features are now always available.
+
       For other changes since CWL v1.0, see the
       [CWL Workflow Description, v1.1 changelog](https://www.commonwl.org/v1.1/Workflow.html#Changelog)
       and
@@ -302,10 +313,6 @@ $graph:
 
     # Merging multiple inbound data links
 
-    To merge multiple inbound data links,
-    [MultipleInputFeatureRequirement](#MultipleInputFeatureRequirement) must be specified
-    in the workflow or workflow step requirements.
-
     If the sink parameter is an array, or named in a [workflow
     scatter](#ScatterWorkflowStep) operation, there may be multiple inbound
     data links listed in the `source` field.  The values from the
@@ -410,9 +417,6 @@ $graph:
         - Expression
       jsonldPredicate: "cwl:valueFrom"
       doc: |
-        To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must
-        be specified in the workflow or workflow step requirements.
-
         If `valueFrom` is a constant string value, use this as the value for
         this input parameter.
 
@@ -470,9 +474,6 @@ $graph:
         - Expression
       jsonldPredicate: "cwl:valueFrom"
       doc: |
-        To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must
-        be specified in the workflow or workflow step requirements.
-
         If `valueFrom` is a constant string value, use this as the value for
         this input parameter.
 
@@ -538,10 +539,6 @@ $graph:
 
     # Subworkflows
 
-    To specify a nested workflow as part of a workflow step,
-    [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) must be
-    specified in the workflow or workflow step requirements.
-
     It is a fatal error if a workflow directly or indirectly invokes itself as
     a subworkflow (recursive workflows are not allowed).
 
@@ -623,10 +620,6 @@ $graph:
   extends: AbstractWorkflowStep
   docParent: "#Workflow"
   doc: |
-    To use scatter/gather,
-    [ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified
-    in the workflow or workflow step requirements.
-
     A "scatter" operation specifies that the associated workflow step or
     subworkflow should execute separately over a list of input elements.  Each
     job making up a scatter operation is independent and may be executed
@@ -813,12 +806,11 @@ $graph:
     * If all workflow steps are executed and complete with `success`, then the
     workflow status is `success`.
 
-    # Extensions
+    # Complex steps
 
-    [ScatterFeatureRequirement](#ScatterFeatureRequirement) and
-    [SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) are
-    available as standard [extensions](#Extensions_and_Metadata) to core
-    workflow semantics.
+    Individual workflow steps may specify complex behavior.  Currently
+    this consists scatter/gather, conditional execution, iterative
+    execution (loops), or executing other workflows.
 
   fields:
     - name: "class"
@@ -847,6 +839,10 @@ $graph:
   name: SubworkflowFeatureRequirement
   extends: ProcessRequirement
   doc: |
+    **Deprecated as of v1.3** This feature is available by default,
+      workflows that use it do not need to declare it.  Including this
+      requirement is a no-op.
+
     Indicates that the workflow platform must support nested workflows in
     the `run` field of [AbstractWorkflowStep](#AbstractWorkflowStep).
   fields:
@@ -865,6 +861,10 @@ $graph:
   type: record
   extends: ProcessRequirement
   doc: |
+    **Deprecated as of v1.3** This feature is available by default,
+      workflows that use it do not need to declare it.  Including this
+      requirement is a no-op.
+
     Indicates that the workflow platform must support the `scatter` and
     `scatterMethod` fields of [ScatterWorkflowStep](#ScatterWorkflowStep).
   fields:
@@ -883,6 +883,10 @@ $graph:
   type: record
   extends: ProcessRequirement
   doc: |
+    **Deprecated as of v1.3** This feature is available by default,
+      workflows that use it do not need to declare it.  Including this
+      requirement is a no-op.
+
     Indicates that the workflow platform must support multiple inbound data links
     listed in the `source` field of [WorkflowStepInput](#WorkflowStepInput).
   fields:
@@ -901,6 +905,10 @@ $graph:
   name: StepInputExpressionRequirement
   extends: ProcessRequirement
   doc: |
+    **Deprecated as of v1.3** This feature is available by default,
+      workflows that use it do not need to declare it.  Including this
+      requirement is a no-op.
+
     Indicate that the workflow platform must support the `valueFrom` field
     of [WorkflowStepInput](#WorkflowStepInput).
   fields: