From 53936b7b68594a8aec4078fbf02fd3291b1f621c Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curii.com>
Date: Thu, 18 Jul 2024 10:14:11 -0400
Subject: [PATCH 1/6] Move initialWorkDir, envDef and networkAccess to
 CommandLineTool

These are core features and using them via 'Requirements' just makes
the syntax awkward.
---
 CommandLineTool.yml | 93 ++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 92 insertions(+), 1 deletion(-)

diff --git a/CommandLineTool.yml b/CommandLineTool.yml
index 604c668..6ba7ae9 100644
--- a/CommandLineTool.yml
+++ b/CommandLineTool.yml
@@ -711,6 +711,91 @@ $graph:
 
         If not specified, all exit codes except 0 are considered permanent failure.
 
+    - name: networkAccess
+      type: [boolean, Expression]
+      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:
+        - 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:
+        mapSubject: envName
+        mapPredicate: envValue
+
+
 
 - type: record
   name: DockerRequirement
@@ -991,7 +1076,9 @@ $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 +1146,8 @@ $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:
@@ -1291,6 +1380,8 @@ $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.

From f68ea3809cbbf7c8d6f074e4093770bc0086073f Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curii.com>
Date: Thu, 18 Jul 2024 10:29:25 -0400
Subject: [PATCH 2/6] Deprecate boilerplate feature requirements and update
 changelog

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 CommandLineTool.yml | 14 ++++++++++++
 Workflow.yml        | 54 ++++++++++++++++++++++++++-------------------
 2 files changed, 45 insertions(+), 23 deletions(-)

diff --git a/CommandLineTool.yml b/CommandLineTool.yml
index 6ba7ae9..4913159 100644
--- a/CommandLineTool.yml
+++ b/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 supercedes the
+        [NetworkAccess](#NetworkAccess) requirement, which is now
+        deprecated.
+      * New field `envDef` on [CommandLineTool](#CommandLineTool).
+        This supercedes the [EnvVarRequirement](#EnvVarRequirement)
+        requirement, which is now deprecated.
+      * New field `initialWorkDir` on
+        [CommandLineTool](#CommandLineTool).  This supercedes 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
diff --git a/Workflow.yml b/Workflow.yml
index 6c20b8c..c303830 100644
--- a/Workflow.yml
+++ b/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:

From 42089d5a9562245ab727aba06cb6ab136a3471fa Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curii.com>
Date: Thu, 18 Jul 2024 10:48:56 -0400
Subject: [PATCH 3/6] Set predicates for networkAccess and envDef

---
 CommandLineTool.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CommandLineTool.yml b/CommandLineTool.yml
index 4913159..9ac851a 100644
--- a/CommandLineTool.yml
+++ b/CommandLineTool.yml
@@ -727,6 +727,7 @@ $graph:
 
     - name: networkAccess
       type: [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
@@ -806,6 +807,7 @@ $graph:
         the execution environment of the tool.  See
         [EnvironmentDef](#EnvironmentDef) for details.
       jsonldPredicate:
+        "_id": "cwl:EnvVarRequirement/envDef"
         mapSubject: envName
         mapPredicate: envValue
 
@@ -1179,6 +1181,7 @@ $graph:
       type: EnvironmentDef[]
       doc: The list of environment variables.
       jsonldPredicate:
+        "_id": "cwl:EnvVarRequirement/envDef"
         mapSubject: envName
         mapPredicate: envValue
 
@@ -1425,6 +1428,7 @@ $graph:
         "_type": "@vocab"
     - name: networkAccess
       type: [boolean, Expression]
+      jsonldPredicate: "cwl:NetworkAccess/networkAccess"
 
 - name: InplaceUpdateRequirement
   type: record

From 094e0bab1b8985b3a059668a095a18408a2d107a Mon Sep 17 00:00:00 2001
From: Peter Amstutz <peter.amstutz@curii.com>
Date: Thu, 18 Jul 2024 11:14:04 -0400
Subject: [PATCH 4/6] Make networkAccess, envDef and initialWorkDir optional

---
 CommandLineTool.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/CommandLineTool.yml b/CommandLineTool.yml
index 9ac851a..09cd1d6 100644
--- a/CommandLineTool.yml
+++ b/CommandLineTool.yml
@@ -726,7 +726,7 @@ $graph:
         If not specified, all exit codes except 0 are considered permanent failure.
 
     - name: networkAccess
-      type: [boolean, Expression]
+      type: ['null', boolean, Expression]
       jsonldPredicate: "cwl:NetworkAccess/networkAccess"
       doc: |
         Indicate whether a process requires outgoing IPv4/IPv6 network
@@ -747,6 +747,7 @@ $graph:
 
     - name: initialWorkDir
       type:
+        - 'null'
         - Expression
         - type: array
           items:
@@ -801,7 +802,7 @@ $graph:
         output directory.
 
     - name: envDef
-      type: EnvironmentDef[]
+      type: EnvironmentDef[]?
       doc: |
         Define a list of environment variables which will be set in
         the execution environment of the tool.  See

From 0a69fcd7254fce6d65ba446407bff4d438cd240d Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Thu, 18 Jul 2024 13:49:26 -0400
Subject: [PATCH 5/6] `networkAcess`, `envDef`, and `initialWorkDir` tests

---
 conformance_tests.yaml                        | 510 +++++++++++++++++-
 tests/dir5_noiwdr.cwl                         |  18 +
 tests/env-tool1_noreq.cwl                     |  16 +
 tests/env-tool4_noreq.cwl                     |  16 +
 tests/env-wf1_noreq.cwl                       |  23 +
 tests/initialwork-path_noiwdr.cwl             |  14 +
 tests/initialworkdir-glob-fullpath_noiwdr.cwl |  26 +
 ...alworkdirrequirement-docker-out_noiwdr.cwl |  30 ++
 tests/inp_update_wf_noiwdr.cwl                |  33 ++
 tests/inpdir_update_wf_noiwdr.cwl             |  42 ++
 tests/iwd/iwd-container-entryname1_noiwdr.cwl |  27 +
 tests/iwd/iwd-container-entryname2_noiwdr.cwl |  21 +
 tests/iwd/iwd-container-entryname3_noiwdr.cwl |  24 +
 tests/iwd/iwd-container-entryname4_noiwdr.cwl |  21 +
 tests/iwd/iwd-fileobjs1_noiwdr.cwl            |  20 +
 tests/iwd/iwd-fileobjs2_noiwdr.cwl            |  18 +
 tests/iwd/iwd-jsondump1-nl_noiwdr.cwl         |  22 +
 tests/iwd/iwd-jsondump1_noiwdr.cwl            |  23 +
 tests/iwd/iwd-jsondump2-nl_noiwdr.cwl         |  23 +
 tests/iwd/iwd-jsondump2_noiwdr.cwl            |  23 +
 tests/iwd/iwd-jsondump3-nl_noiwdr.cwl         |  19 +
 tests/iwd/iwd-jsondump3_noiwdr.cwl            |  19 +
 tests/iwd/iwd-nolimit_noiwdr.cwl              |  24 +
 tests/iwd/iwd-passthrough1_noreq.cwl          |  22 +
 tests/iwd/iwd-passthrough2_noiwdr.cwl         |  29 +
 tests/iwd/iwd-passthrough3_noreq.cwl          |  15 +
 tests/iwd/iwd-passthrough4_noreq.cwl          |  14 +
 tests/iwd/iwd-passthrough5_noreq.cwl          |  15 +
 tests/iwd/iwd-subdir-tool_noreq.cwl           |  15 +
 tests/iwd/iwd-subdir-wf_noreq.cwl             |  19 +
 tests/iwd/iwd_dir_literal_real_file.cwl       |  25 +
 tests/iwd/test-index.yaml                     | 323 ++++++++++-
 tests/iwdr-entry_noreq.cwl                    |  18 +
 tests/iwdr_with_nested_dirs_noreq.cwl         |  39 ++
 tests/linkfile_noreq.cwl                      |  20 +
 tests/networkaccess_noreq.cwl                 |  14 +
 tests/recursive-input-directory_noiwdr.cwl    |  33 ++
 tests/rename_noreq.cwl                        |  14 +
 tests/search_noiwdr.cwl                       | 109 ++++
 .../secondaryfiles/rename-outputs_noiwdr.cwl  |  49 ++
 tests/secondaryfiles/test-index.yaml          |  20 +-
 tests/stage-array-dirs_noreq.cwl              |  20 +
 tests/stage-array_noiwdr.cwl                  |  32 ++
 ...le_array_basename_and_entryname_noiwdr.cwl |  23 +
 tests/stage_file_array_noiwdr.cwl             |  23 +
 tests/stagefile_noreq.cwl                     |  25 +
 .../bash-dollar-quote_noiwdr.cwl              |  56 ++
 ...ine-continuation-with-expression_noreq.cwl |  20 +
 .../bash-line-continuation_noreq.cwl          |  17 +
 .../string-interpolation/js-quote_noiwdr.cwl  |  36 ++
 tests/string-interpolation/test-index.yaml    |  62 ++-
 tests/template-tool_noiwdr.cwl                |  25 +
 tests/updatedir_inplace_noiwdr.cwl            |  20 +
 tests/updateval_inplace_noiwdr.cwl            |  27 +
 tests/writable-dir-docker_noiwdr.cwl          |  23 +
 tests/writable-dir_noiwdr.cwl                 |  17 +
 56 files changed, 2203 insertions(+), 28 deletions(-)
 create mode 100644 tests/dir5_noiwdr.cwl
 create mode 100644 tests/env-tool1_noreq.cwl
 create mode 100644 tests/env-tool4_noreq.cwl
 create mode 100644 tests/env-wf1_noreq.cwl
 create mode 100644 tests/initialwork-path_noiwdr.cwl
 create mode 100644 tests/initialworkdir-glob-fullpath_noiwdr.cwl
 create mode 100644 tests/initialworkdirrequirement-docker-out_noiwdr.cwl
 create mode 100644 tests/inp_update_wf_noiwdr.cwl
 create mode 100644 tests/inpdir_update_wf_noiwdr.cwl
 create mode 100644 tests/iwd/iwd-container-entryname1_noiwdr.cwl
 create mode 100644 tests/iwd/iwd-container-entryname2_noiwdr.cwl
 create mode 100644 tests/iwd/iwd-container-entryname3_noiwdr.cwl
 create mode 100644 tests/iwd/iwd-container-entryname4_noiwdr.cwl
 create mode 100644 tests/iwd/iwd-fileobjs1_noiwdr.cwl
 create mode 100644 tests/iwd/iwd-fileobjs2_noiwdr.cwl
 create mode 100644 tests/iwd/iwd-jsondump1-nl_noiwdr.cwl
 create mode 100644 tests/iwd/iwd-jsondump1_noiwdr.cwl
 create mode 100644 tests/iwd/iwd-jsondump2-nl_noiwdr.cwl
 create mode 100644 tests/iwd/iwd-jsondump2_noiwdr.cwl
 create mode 100644 tests/iwd/iwd-jsondump3-nl_noiwdr.cwl
 create mode 100644 tests/iwd/iwd-jsondump3_noiwdr.cwl
 create mode 100644 tests/iwd/iwd-nolimit_noiwdr.cwl
 create mode 100644 tests/iwd/iwd-passthrough1_noreq.cwl
 create mode 100644 tests/iwd/iwd-passthrough2_noiwdr.cwl
 create mode 100644 tests/iwd/iwd-passthrough3_noreq.cwl
 create mode 100644 tests/iwd/iwd-passthrough4_noreq.cwl
 create mode 100644 tests/iwd/iwd-passthrough5_noreq.cwl
 create mode 100644 tests/iwd/iwd-subdir-tool_noreq.cwl
 create mode 100644 tests/iwd/iwd-subdir-wf_noreq.cwl
 create mode 100644 tests/iwd/iwd_dir_literal_real_file.cwl
 create mode 100644 tests/iwdr-entry_noreq.cwl
 create mode 100644 tests/iwdr_with_nested_dirs_noreq.cwl
 create mode 100644 tests/linkfile_noreq.cwl
 create mode 100644 tests/networkaccess_noreq.cwl
 create mode 100644 tests/recursive-input-directory_noiwdr.cwl
 create mode 100644 tests/rename_noreq.cwl
 create mode 100644 tests/search_noiwdr.cwl
 create mode 100644 tests/secondaryfiles/rename-outputs_noiwdr.cwl
 create mode 100644 tests/stage-array-dirs_noreq.cwl
 create mode 100644 tests/stage-array_noiwdr.cwl
 create mode 100644 tests/stage_file_array_basename_and_entryname_noiwdr.cwl
 create mode 100644 tests/stage_file_array_noiwdr.cwl
 create mode 100644 tests/stagefile_noreq.cwl
 create mode 100644 tests/string-interpolation/bash-dollar-quote_noiwdr.cwl
 create mode 100644 tests/string-interpolation/bash-line-continuation-with-expression_noreq.cwl
 create mode 100644 tests/string-interpolation/bash-line-continuation_noreq.cwl
 create mode 100644 tests/string-interpolation/js-quote_noiwdr.cwl
 create mode 100755 tests/template-tool_noiwdr.cwl
 create mode 100755 tests/updatedir_inplace_noiwdr.cwl
 create mode 100755 tests/updateval_inplace_noiwdr.cwl
 create mode 100644 tests/writable-dir-docker_noiwdr.cwl
 create mode 100644 tests/writable-dir_noiwdr.cwl

diff --git a/conformance_tests.yaml b/conformance_tests.yaml
index 21f7d7f..a54dd07 100644
--- a/conformance_tests.yaml
+++ b/conformance_tests.yaml
@@ -431,7 +431,7 @@
       size: 15
   tool: tests/env-wf1.cwl
   id: requirement_priority
-  doc: Test requirement priority
+  doc: Test requirement priority using nested EnvVarRequirements
   tags: [ env_var, workflow ]
 
 - job: tests/env-job.json
@@ -614,7 +614,7 @@
         size: 16
   tool: tests/iwdr-entry.cwl
   id: initial_workdir_trailingnl
-  doc: Test if trailing newline is present in file entry in InitialWorkDir
+  doc: Test if trailing newline is present in file entry in InitialWorkDirRequirement
   tags: [ initial_work_dir, command_line_tool ]
 
 - job: tests/wc-job.json
@@ -1174,7 +1174,7 @@
   }
   tool: tests/dir5.cwl
   id: dynamic_initial_workdir
-  doc: Test dynamic initial work dir
+  doc: Test dynamic InitialWorkDirRequirement
   tags: [ shell_command, initial_work_dir, command_line_tool ]
 
 - job: tests/stagefile-job.yml
@@ -1188,7 +1188,7 @@
   }
   tool: tests/stagefile.cwl
   id: writable_stagedfiles
-  doc: Test writable staged files.
+  doc: Test writable staged files using InitialWorkDirRequirement.
   tags: [ initial_work_dir, command_line_tool ]
 
 - job: tests/file-literal.yml
@@ -1212,7 +1212,7 @@
         size: 0
   tool: tests/linkfile.cwl
   id: initial_workdir_expr
-  doc: Test expression in InitialWorkDir listing
+  doc: Test expression in InitialWorkDirRequirement listing
   tags: [ initial_work_dir, command_line_tool ]
 
 - job: tests/wc-job.json
@@ -1476,7 +1476,7 @@
       }
   tool: tests/recursive-input-directory.cwl
   id: input_dir_recurs_copy_writable
-  doc: Test if a writable input directory is recursively copied and writable
+  doc: Test if a writable IWDR input directory is recursively copied and writable
   tags: [ initial_work_dir, shell_command, command_line_tool ]
 
 - output:
@@ -1530,7 +1530,7 @@
   output: {}
   tool: tests/initialwork-path.cwl
   id: initialworkpath_output
-  doc: Test that file path in $(inputs) for initialworkdir is in $(outdir).
+  doc: Test that file path in $(inputs) for initialWorkDirRequirement is in $(outdir).
   tags: [ initial_work_dir, command_line_tool ]
 
 - job: tests/count-lines6-job.json
@@ -2751,7 +2751,7 @@
 - job: tests/empty.json
   output: {}
   tool: tests/networkaccess.cwl
-  doc: Test networkaccess enabled
+  doc: Test networkaccess enabled using the NetworkAccess requirement
   id: networkaccess
   tags: [ command_line_tool, networkaccess ]
 
@@ -2808,7 +2808,7 @@
   tool: tests/env-tool3.cwl
   id: cwl_requirements_addition
   doc: Test requirements in input document via EnvVarRequirement
-  tags: [ command_line_tool, input_object_requirements ]
+  tags: [ command_line_tool, input_object_requirements, env_var ]
 
 - job: tests/env-job3.yaml
   output:
@@ -2820,7 +2820,7 @@
   tool: tests/env-tool4.cwl
   id: cwl_requirements_override_expression
   doc: Test conflicting requirements in input document via EnvVarRequirement and expression
-  tags: [ command_line_tool, input_object_requirements ]
+  tags: [ command_line_tool, input_object_requirements, env_var ]
 
 - job: tests/env-job4.yaml
   output:
@@ -2832,7 +2832,7 @@
   id: cwl_requirements_override_static
   tool: tests/env-tool3.cwl
   doc: Test conflicting requirements in input document via EnvVarRequirement
-  tags: [ command_line_tool, input_object_requirements ]
+  tags: [ command_line_tool, input_object_requirements, env_var ]
 
 - job: tests/initialworkdirrequirement-docker-out-job.json
   output:
@@ -2849,7 +2849,7 @@
       "size": 12010
   tool: tests/initialworkdir-glob-fullpath.cwl
   id: initial_workdir_output_glob
-  doc: Test full path glob output of InitialWorkDir
+  doc: Test full path glob output of InitialWorkDirRequirement
   tags: [ initial_work_dir, command_line_tool ]
 
 - job: tests/empty.json
@@ -2886,8 +2886,8 @@
 
 - job: tests/empty.json
   tool: tests/inp_update_wf.cwl
-  doc: inplace update has side effect on file content
-  tags: [ inplace_update, workflow ]
+  doc: inplace update has side effect on file content (using InitialWorkDirRequirement)
+  tags: [ inplace_update, workflow, initial_work_dir ]
   output:
     a: 4
     b: 4
@@ -2895,8 +2895,8 @@
 
 - job: tests/empty.json
   tool: tests/inpdir_update_wf.cwl
-  doc: inplace update has side effect on directory content
-  tags: [ inplace_update, workflow ]
+  doc: inplace update has side effect on directory content (using InitialWorkDirRequirement)
+  tags: [ inplace_update, workflow, initial_work_dir ]
   output: {
     a: [
             {
@@ -2932,7 +2932,7 @@
           listing: []
   tags: [ required, command_line_tool ]
 
-- doc: Test that array of input files can be staged to directory with entryname
+- doc: Test that array of input files can be staged to directory with InitialWorkDirRequirement entryname
   id: stage_file_array
   tool: tests/stage_file_array.cwl
   job: tests/stage_file_array.job.json
@@ -3000,7 +3000,7 @@
       ]
   tags: [ command_line_tool, initial_work_dir, inline_javascript ]
 
-- doc: Test that if array of input files are staged to directory with basename and entryname, entryname overrides
+- doc: Test that if array of input files are staged using InitialWorkDirRequirement to directory with basename and entryname, entryname overrides
   id: stage_file_array_entryname_overrides
   tool: tests/stage_file_array_basename_and_entryname.cwl
   job: tests/stage_file_array.job.json
@@ -3633,3 +3633,477 @@
   tags: [ command_line_tool, inline_javascript, schema_def, initial_work_dir ]
 
 - $import: tests/loop/test-index.yaml
+
+- job: tests/empty.json
+  output: {}
+  tool: tests/networkaccess_noreq.cwl
+  doc: Test networkAcccess enabled using the networkAccess field
+  id: networkaccess_noreq
+  tags: [ command_line_tool, networkaccess ]
+
+- job: tests/env-job.json
+  output:
+    out:
+      class: File
+      checksum: sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519
+      location: out
+      size: 15
+  tool: tests/env-tool1_noreq.cwl
+  id: envvar_noreq
+  doc: Test CommandLineTool.envDef
+  tags: [ env_var, command_line_tool ]
+
+- job: tests/env-job.json
+  output:
+    out:
+      class: File
+      checksum: sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519
+      location: out
+      size: 15
+  tool: tests/env-wf1_noreq.cwl
+  id: requirement_priority_noreq
+  doc: |
+    Test requirement priority: EnvVarRequirement + CommandLineTool.envDef
+  tags: [ env_var, workflow ]
+
+- job: tests/env-job3.yaml
+  output:
+    out:
+      class: File
+      checksum: sha1$b3ec4ed1749c207e52b3a6d08c59f31d83bff519
+      location: out
+      size: 15
+  tool: tests/env-tool4_noreq.cwl
+  id: cwl_envdef_override_expression
+  doc: Test conflicting requirements in input document via envDef and expression
+  tags: [ command_line_tool, input_object_requirements, env_var ]
+
+- job: tests/dir-job.yml
+  output: {
+    "outlist": {
+        "checksum": "sha1$13cda8661796ae241da3a18668fb552161a72592",
+        "size": 20,
+        "location": "output.txt",
+        "class": "File"
+    }
+  }
+  tool: tests/dir5_noiwdr.cwl
+  id: dynamic_initial_workdir_noreq
+  doc: Test dynamic initialWorkDir
+  tags: [ shell_command, initial_work_dir, command_line_tool ]
+
+- job: tests/initialworkdirrequirement-docker-out-job.json
+  output:
+    OUTPUT:
+      "checksum": "sha1$aeb3d11bdf536511649129f4077d5cda6a324118"
+      "location": "ref.fasta"
+      "secondaryFiles": [{
+        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+        "location": "ref.fasta.fai",
+          "class": "File",
+          "size": 0
+      }]
+      "class": "File"
+      "size": 12010
+  tool: tests/initialworkdir-glob-fullpath_noiwdr.cwl
+  id: initial_workdir_output_glob_noreq
+  doc: Test full path glob output of initialWorkDir
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: tests/wc-job.json
+  output: {}
+  tool: tests/initialwork-path_noiwdr.cwl
+  id: initialworkpath_output_noreq
+  doc: Test that file path in $(inputs) for initialWorkDir is in $(outdir).
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: tests/string-job.json
+  output:
+    out:
+        class: File
+        checksum: sha1$6a47aa22b2a9d13a66a24b3ee5eaed95ce4753cf
+        location: example.conf
+        size: 16
+  tool: tests/iwdr-entry_noreq.cwl
+  id: initial_workdir_trailingnl_noreq
+  doc: Test if trailing newline is present in file entry in initialWorkDir
+  tags: [ initial_work_dir, command_line_tool ]
+
+- doc: Test initialWorkDir with a nested directory structure from another step
+  job: tests/empty.json
+  output:
+    ya_empty:
+      class: File
+      checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
+      location: ya
+      size: 0
+  tool: tests/iwdr_with_nested_dirs_noreq.cwl
+  id: initialworkdir_nesteddir_noreq
+  tags: [ initial_work_dir, workflow ]
+
+- job: tests/arguments-job.yml
+  output:
+    classfile:
+        checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
+        location: Hello.class
+        class: File
+        size: 0
+  tool: tests/linkfile_noreq.cwl
+  id: initial_workdir_expr_noreq
+  doc: Test expression in initialWorkDir
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: tests/recursive-input-directory.yml
+  output:
+    output_dir: {
+        "basename": "work_dir",
+        "class": "Directory",
+        "listing": [
+            {
+                "basename": "a",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "class": "File",
+                "location": "work_dir/a",
+                "size": 0
+            },
+            {
+                "basename": "b",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "class": "File",
+                "location": "work_dir/b",
+                "size": 0
+            },
+            {
+                "basename": "c",
+                "class": "Directory",
+                "listing": [
+                    {
+                        "basename": "d",
+                        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                        "class": "File",
+                        "location": "work_dir/c/d",
+                        "size": 0
+                    }
+                ],
+                "location": "work_dir/c",
+            },
+            {
+                "basename": "e",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "class": "File",
+                "location": "work_dir/e",
+                "size": 0
+            },
+        ],
+        "location": "work_dir",
+      }
+    test_result: {
+        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+        "class": "File",
+        "location": "output.txt",
+        "size": 0
+      }
+  tool: tests/recursive-input-directory_noiwdr.cwl
+  id: input_dir_recurs_copy_writable_noiwdr
+  doc: Test if a writable initialWorkDir input directory is recursively copied and writable
+  tags: [ initial_work_dir, shell_command, command_line_tool ]
+
+- job: tests/rename-job.json
+  output:
+    outfile:
+      class: File
+      checksum: sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376
+      location: fish.txt
+      size: 1111
+  tool: tests/rename_noreq.cwl
+  id: rename_noreq
+  doc: >-
+    Test initialWorkDir with expression in filename.
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: tests/search-job.json
+  output:
+    outfile:
+      class: File
+      checksum: sha1$e2dc9daaef945ac15f01c238ed2f1660f60909a0
+      location: result.txt
+      size: 142
+    indexedfile: {
+        "location": "input.txt",
+        "class": "File",
+        "checksum": "sha1$327fc7aedf4f6b69a42a7c8b808dc5a7aff61376",
+        "secondaryFiles": [
+            {
+                "location": "input.txt.idx1",
+                "class": "File",
+                "checksum": "sha1$1f6fe811644355974cdd06d9eb695d6e859f3b44",
+                "size": 1500
+            },
+            {
+                "location": "input.idx2",
+                "class": "File",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "size": 0
+            },
+            {
+                "location": "input.txt.idx3",
+                "class": "File",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "size": 0
+            },
+            {
+                "location": "input.txt.idx4",
+                "class": "File",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "size": 0
+            },
+            {
+                "location": "input.txt.idx5",
+                "class": "File",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "size": 0
+            },
+            {
+                "location": "input.idx6.txt",
+                "class": "File",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "size": 0
+            },
+            {
+            "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+            "class": "File",
+            "location": "input.txt.idx7",
+            "size": 0
+            },
+            {
+            "checksum": "sha1$47a013e660d408619d894b20806b1d5086aab03b",
+            "class": "File",
+            "location": "hello.txt",
+            "size": 13
+            },
+            {
+            "class": "Directory",
+            "listing": [{
+               "basename": "index",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "class": "File",
+                "location": "index",
+                "size": 0
+            }],
+            "location": "input.txt_idx8",
+          }
+        ],
+        "size": 1111
+    }
+  tool: "tests/search_noiwdr.cwl#main"
+  id: initial_workdir_secondary_files_expr_noiwdr
+  doc: >-
+    Test initialWorkDir linking input files and capturing secondaryFiles
+    on input and output. Also tests the use of a variety of parameter references
+    and expressions in the secondaryFiles field.
+  tags: [ initial_work_dir, inline_javascript, workflow ]
+
+- job: tests/stage-array-job.json
+  tool: tests/stage-array_noiwdr.cwl
+  doc: Test null and array input in initialWorkDir
+  output:
+      "output": {
+        "basename": "lsout",
+        "checksum": "sha1$e453d26efd859a9abc80ae1a1d9d63db72376053",
+        "class": "File",
+        "location": "lsout",
+        "size": 32
+      }
+  tags: [ resource, command_line_tool, initial_work_dir ]
+  id: initial_work_dir_for_null_and_arrays_noreq
+
+- job: tests/stage-array-dirs-job.yml
+  tool: tests/stage-array-dirs_noreq.cwl
+  doc: Test array of directories initialWorkDir
+  output: {
+    "output": [
+            {
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "class": "File",
+                "location": "a",
+                "size": 0
+            },
+            {
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "class": "File",
+                "location": "B",
+                "size": 0
+            }
+        ]
+    }
+  tags: [ resource, command_line_tool, initial_work_dir ]
+  id: initial_work_dir_for_array_dirs_noreq
+
+- doc: Test that array of input files can be staged to directory with initialWorkDir.entryname
+  id: stage_file_array_noiwdr
+  tool: tests/stage_file_array_noiwdr.cwl
+  job: tests/stage_file_array.job.json
+  output:
+    output:
+      [
+        {
+          "basename": "sfa-1.txt",
+          "checksum": "sha1$4c1cd0638ab3580310823fd1556d27ecb4816df6",
+          "class": "File",
+          "size": 49
+        },
+        {
+          "basename": "sfa-1.txt.sec",
+          "checksum": "sha1$40f4ee1bcd1a9466fcd2e48cf7fc3798025d2f9a",
+          "class": "File",
+          "size": 59
+        },
+        {
+          "basename": "sfa-2.txt",
+          "checksum": "sha1$4c1cd0638ab3580310823fd1556d27ecb4816df6",
+          "class": "File",
+          "size": 49
+        },
+        {
+          "basename": "sfa-2.txt.sec",
+          "checksum": "sha1$40f4ee1bcd1a9466fcd2e48cf7fc3798025d2f9a",
+          "class": "File",
+          "size": 59
+        }
+      ]
+  tags: [ command_line_tool, initial_work_dir, inline_javascript ]
+
+- doc: Test that if array of input files are staged using initialWorkDir to a directory with basename and entryname, entryname overrides
+  id: stage_file_array_entryname_overrides_noiwdr
+  tool: tests/stage_file_array_basename_and_entryname_noiwdr.cwl
+  job: tests/stage_file_array.job.json
+  output:
+    output:
+      [
+        {
+          "basename": "sfa-1.txt",
+          "checksum": "sha1$4c1cd0638ab3580310823fd1556d27ecb4816df6",
+          "class": "File",
+          "size": 49
+        },
+        {
+          "basename": "sfa-1.txt.sec",
+          "checksum": "sha1$40f4ee1bcd1a9466fcd2e48cf7fc3798025d2f9a",
+          "class": "File",
+          "size": 59
+        },
+        {
+          "basename": "sfa-2.txt",
+          "checksum": "sha1$4c1cd0638ab3580310823fd1556d27ecb4816df6",
+          "class": "File",
+          "size": 49
+        },
+        {
+          "basename": "sfa-2.txt.sec",
+          "checksum": "sha1$40f4ee1bcd1a9466fcd2e48cf7fc3798025d2f9a",
+          "class": "File",
+          "size": 59
+        }
+      ]
+  tags: [ command_line_tool, initial_work_dir, inline_javascript ]
+
+- job: tests/stagefile-job.yml
+  output: {
+    "outfile": {
+        "checksum": "sha1$b769c7b2e316edd4b5eb2d24799b2c1f9d8c86e6",
+        "size": 1111,
+        "location": "bob.txt",
+        "class": "File"
+    }
+  }
+  tool: tests/stagefile_noreq.cwl
+  id: writable_stagedfiles_noreq
+  doc: Test writable staged files using initialWorkDir.
+  tags: [ initial_work_dir, command_line_tool ]
+
+- output:
+    "foo": {
+        "checksum": "sha1$63da67422622fbf9251a046d7a34b7ea0fd4fead",
+        "class": "File",
+        "location": "foo.txt",
+        "size": 22
+    }
+  job: tests/cat-job.json
+  tool: tests/template-tool_noiwdr.cwl
+  id: initworkdir_expreng_requirements_noiwdr
+  doc: Test initialWorkDir ExpressionEngineRequirement.engineConfig feature
+  tags: [ initial_work_dir, inline_javascript, command_line_tool ]
+
+- job: tests/empty.json
+  tool: tests/inpdir_update_wf_noiwdr.cwl
+  doc: inplace update has side effect on directory content (using initialWorkDir)
+  tags: [ inplace_update, workflow, initial_work_dir ]
+  output: {
+    a: [
+            {
+                "basename": "blurb",
+                "class": "File",
+                "location": "blurb"
+            }
+        ],
+    b: [
+            {
+                "basename": "blurb",
+                "class": "File",
+                "location": "blurb"
+            }
+        ]
+  }
+  id: modify_directory_content_noiwdr
+
+- job: tests/empty.json
+  tool: tests/inp_update_wf_noiwdr.cwl
+  doc: inplace update has side effect on file content (using initialWorkDir)
+  tags: [ inplace_update, workflow, initial_work_dir ]
+  output:
+    a: 4
+    b: 4
+  id: modify_file_content
+
+- job: tests/empty.json
+  output:
+    out: {
+        "basename": "emptyWritableDir",
+        "listing": [
+            {
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "basename": "blurg",
+                "location": "blurg",
+                "class": "File",
+                "size": 0
+            }
+        ],
+        "location": "emptyWritableDir",
+        "class": "Directory"
+    }
+  tool: tests/writable-dir_noiwdr.cwl
+  id: initial_workdir_empty_writable_noiwdr
+  doc: Test empty writable dir with initialWorkDir
+  tags: [ inline_javascript, initial_work_dir, command_line_tool ]
+
+
+- job: tests/empty.json
+  output:
+    out: {
+        "basename": "emptyWritableDir",
+        "listing": [
+            {
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "basename": "blurg",
+                "location": "blurg",
+                "class": "File",
+                "size": 0
+            }
+        ],
+        "location": "emptyWritableDir",
+        "class": "Directory"
+    }
+  tool: tests/writable-dir-docker_noiwdr.cwl
+  id: initial_workdir_empty_writable_docker_noiwdr
+  doc: Test empty writable dir with initialWorkDir inside Docker
+  tags: [ inline_javascript, initial_work_dir, command_line_tool ]
diff --git a/tests/dir5_noiwdr.cwl b/tests/dir5_noiwdr.cwl
new file mode 100644
index 0000000..485b90e
--- /dev/null
+++ b/tests/dir5_noiwdr.cwl
@@ -0,0 +1,18 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+requirements:
+  - class: ShellCommandRequirement
+initialWorkDir: $(inputs.indir.listing)
+inputs:
+  indir:
+    type: Directory
+    loadListing: shallow_listing
+outputs:
+  outlist:
+    type: File
+    outputBinding:
+      glob: output.txt
+arguments: ["find", "-L", ".", "!", "-path", "*.txt",
+  {shellQuote: false, valueFrom: "|"},
+  "sort"]
+stdout: output.txt
diff --git a/tests/env-tool1_noreq.cwl b/tests/env-tool1_noreq.cwl
new file mode 100644
index 0000000..4551536
--- /dev/null
+++ b/tests/env-tool1_noreq.cwl
@@ -0,0 +1,16 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+inputs:
+  in: string
+outputs:
+  out:
+    type: File
+    outputBinding:
+      glob: out
+
+envDef:
+  TEST_ENV: $(inputs.in)
+
+baseCommand: ["/bin/sh", "-c", "echo $TEST_ENV"]
+
+stdout: out
diff --git a/tests/env-tool4_noreq.cwl b/tests/env-tool4_noreq.cwl
new file mode 100644
index 0000000..8393cb0
--- /dev/null
+++ b/tests/env-tool4_noreq.cwl
@@ -0,0 +1,16 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+inputs:
+  in: string
+outputs:
+  out:
+    type: File
+    outputBinding:
+      glob: out
+
+envDef:
+  TEST_ENV: conflict_original
+
+baseCommand: ["/bin/bash", "-c", "echo $TEST_ENV"]
+
+stdout: out
diff --git a/tests/env-wf1_noreq.cwl b/tests/env-wf1_noreq.cwl
new file mode 100644
index 0000000..da1c032
--- /dev/null
+++ b/tests/env-wf1_noreq.cwl
@@ -0,0 +1,23 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.3.0-dev1
+
+inputs:
+    in: string
+
+outputs:
+    out:
+      type: File
+      outputSource: step1/out
+
+requirements:
+  EnvVarRequirement:
+    envDef:
+      TEST_ENV: override
+
+steps:
+  step1:
+    run: env-tool1_noreq.cwl
+    in:
+      in: in
+    out: [out]
diff --git a/tests/initialwork-path_noiwdr.cwl b/tests/initialwork-path_noiwdr.cwl
new file mode 100644
index 0000000..e89d86f
--- /dev/null
+++ b/tests/initialwork-path_noiwdr.cwl
@@ -0,0 +1,14 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+requirements:
+  ShellCommandRequirement: {}
+initialWorkDir:
+  - entry: $(inputs.file1)
+    entryname: bob.txt
+inputs:
+  file1: File
+outputs: []
+arguments:
+  - shellQuote: false
+    valueFrom: |
+      test "$(inputs.file1.path)" = "$(runtime.outdir)/bob.txt"
diff --git a/tests/initialworkdir-glob-fullpath_noiwdr.cwl b/tests/initialworkdir-glob-fullpath_noiwdr.cwl
new file mode 100644
index 0000000..7b8c0a7
--- /dev/null
+++ b/tests/initialworkdir-glob-fullpath_noiwdr.cwl
@@ -0,0 +1,26 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.3.0-dev1
+
+initialWorkDir:
+  - $(inputs.INPUT)
+
+class: CommandLineTool
+
+inputs:
+  - id: INPUT
+    type: File
+
+outputs:
+  - id: OUTPUT
+    type: File
+    outputBinding:
+      glob: $(runtime.outdir)/$(inputs.INPUT.basename)
+    secondaryFiles:
+      - .fai
+
+arguments:
+  - valueFrom: $(inputs.INPUT.basename).fai
+    position: 0
+
+baseCommand: [touch]
diff --git a/tests/initialworkdirrequirement-docker-out_noiwdr.cwl b/tests/initialworkdirrequirement-docker-out_noiwdr.cwl
new file mode 100644
index 0000000..7898665
--- /dev/null
+++ b/tests/initialworkdirrequirement-docker-out_noiwdr.cwl
@@ -0,0 +1,30 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.3.0-dev1
+
+requirements:
+  - class: DockerRequirement
+    dockerPull: docker.io/debian:stable-slim
+
+initialWorkDir:    
+  - $(inputs.INPUT)
+
+class: CommandLineTool
+
+inputs:
+  - id: INPUT
+    type: File
+
+outputs:
+  - id: OUTPUT
+    type: File
+    outputBinding:
+      glob: $(inputs.INPUT.basename)
+    secondaryFiles:
+      - .fai
+
+arguments:
+  - valueFrom: $(inputs.INPUT.basename).fai
+    position: 0
+
+baseCommand: [touch]
diff --git a/tests/inp_update_wf_noiwdr.cwl b/tests/inp_update_wf_noiwdr.cwl
new file mode 100644
index 0000000..fe86e5c
--- /dev/null
+++ b/tests/inp_update_wf_noiwdr.cwl
@@ -0,0 +1,33 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.3.0-dev1
+inputs: []
+outputs:
+  a:
+    type: int
+    outputSource: step3/output
+  b:
+    type: int
+    outputSource: step4/output
+steps:
+  step1:
+    in:
+      in: {default: "3"}
+    out: [out]
+    run: echo-file-tool.cwl
+  step2:
+    in:
+      r: step1/out
+    out: [out]
+    run: updateval_inplace_noiwdr.cwl
+  step3:
+    in:
+      file1: step1/out
+      wait: step2/out
+    out: [output]
+    run: parseInt-tool.cwl
+  step4:
+    in:
+      file1: step2/out
+    out: [output]
+    run: parseInt-tool.cwl
diff --git a/tests/inpdir_update_wf_noiwdr.cwl b/tests/inpdir_update_wf_noiwdr.cwl
new file mode 100644
index 0000000..2e539a4
--- /dev/null
+++ b/tests/inpdir_update_wf_noiwdr.cwl
@@ -0,0 +1,42 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.3.0-dev1
+inputs: []
+requirements:
+  InlineJavascriptRequirement: {}
+outputs:
+  a:
+    type: File[]
+    outputSource: step3/d1out
+  b:
+    type: File[]
+    outputSource: step3/d2out
+steps:
+  step1:
+    in:
+      dirname: {default: step1dir}
+    out: [out]
+    run: mkdir.cwl
+  step2:
+    in:
+      r: step1/out
+    out: [out]
+    run: updatedir_inplace_noiwdr.cwl
+  step3:
+    in:
+      d1: step1/out
+      d2: step2/out
+    out: [d1out, d2out]
+    run:
+      class: ExpressionTool
+      inputs:
+        d1:
+          type: Directory
+          loadListing: shallow_listing
+        d2:
+          type: Directory
+          loadListing: shallow_listing
+      outputs:
+        d1out: File[]
+        d2out: File[]
+      expression: "$({d1out: inputs.d1.listing, d2out: inputs.d2.listing})"
diff --git a/tests/iwd/iwd-container-entryname1_noiwdr.cwl b/tests/iwd/iwd-container-entryname1_noiwdr.cwl
new file mode 100644
index 0000000..3b861e6
--- /dev/null
+++ b/tests/iwd/iwd-container-entryname1_noiwdr.cwl
@@ -0,0 +1,27 @@
+cwlVersion: v1.3.0-dev1
+class: CommandLineTool
+doc: |
+  When executing in a container, entryname can have an absolute path
+  to a mount location inside the container.
+
+inputs:
+  filelist: File
+
+outputs:
+  head:
+    type: File
+    outputBinding:
+      glob: head.txt
+
+requirements:
+  DockerRequirement:
+    dockerPull: docker.io/debian:stable-slim
+    dockerOutputDirectory: /output
+  ShellCommandRequirement: {}
+
+initialWorkDir:
+  - entryname: /tmp2j3y7rpb/input/stuff.txt  # Give it a weird prefix to minimize chance of conflict with a real file
+    entry: $(inputs.filelist)
+
+arguments:
+  - {shellQuote: false, valueFrom: "head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt"}
diff --git a/tests/iwd/iwd-container-entryname2_noiwdr.cwl b/tests/iwd/iwd-container-entryname2_noiwdr.cwl
new file mode 100644
index 0000000..b06a72c
--- /dev/null
+++ b/tests/iwd/iwd-container-entryname2_noiwdr.cwl
@@ -0,0 +1,21 @@
+cwlVersion: v1.3.0-dev1
+class: CommandLineTool
+doc: |
+  Must fail if entryname is an absolute path and DockerRequirement is
+  not in the 'requirements' section.
+inputs:
+  filelist: File
+outputs:
+  head:
+    type: File
+    outputBinding:
+      glob: head.txt
+requirements:
+  ShellCommandRequirement: {}
+
+initialWorkDir:
+  - entryname: /tmp2j3y7rpb/input/stuff.txt  # Give it a weird prefix to minimize chance of conflict with a real file
+    entry: $(inputs.filelist)
+
+arguments:
+  - {shellQuote: false, valueFrom: "head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt"}
diff --git a/tests/iwd/iwd-container-entryname3_noiwdr.cwl b/tests/iwd/iwd-container-entryname3_noiwdr.cwl
new file mode 100644
index 0000000..4e63e48
--- /dev/null
+++ b/tests/iwd/iwd-container-entryname3_noiwdr.cwl
@@ -0,0 +1,24 @@
+cwlVersion: v1.3.0-dev1
+class: CommandLineTool
+doc: |
+  Must fail if entryname is an absolute path and DockerRequirement is
+  not in the 'requirements' section.
+inputs:
+  filelist: File
+outputs:
+  head:
+    type: File
+    outputBinding:
+      glob: head.txt
+hints:
+  DockerRequirement:
+    dockerPull: docker.io/debian:stable-slim
+    dockerOutputDirectory: /output
+requirements:
+  ShellCommandRequirement: {}
+
+initialWorkDir:
+  - entryname: /tmp2j3y7rpb/input/stuff.txt  # Give it a weird prefix to minimize chance of conflict with a real file
+    entry: $(inputs.filelist)
+arguments:
+  - {shellQuote: false, valueFrom: "head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt"}
diff --git a/tests/iwd/iwd-container-entryname4_noiwdr.cwl b/tests/iwd/iwd-container-entryname4_noiwdr.cwl
new file mode 100644
index 0000000..1f866d9
--- /dev/null
+++ b/tests/iwd/iwd-container-entryname4_noiwdr.cwl
@@ -0,0 +1,21 @@
+cwlVersion: v1.3.0-dev1
+class: CommandLineTool
+doc: |
+  Must fail if entryname starts with ../
+inputs:
+  filelist: File
+outputs:
+  head:
+    type: File
+    outputBinding:
+      glob: head.txt
+
+initialWorkDir:
+  - entryname: ../input/stuff.txt  # Illegal
+    entry: $(inputs.filelist)
+
+requirements:
+  ShellCommandRequirement: {}
+
+arguments:
+  - {shellQuote: false, valueFrom: "head -n10 ../input/stuff.txt > head.txt"}
diff --git a/tests/iwd/iwd-fileobjs1_noiwdr.cwl b/tests/iwd/iwd-fileobjs1_noiwdr.cwl
new file mode 100644
index 0000000..3f87a30
--- /dev/null
+++ b/tests/iwd/iwd-fileobjs1_noiwdr.cwl
@@ -0,0 +1,20 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+doc: Can have a file declared directly in an initialWorkDir
+initialWorkDir:
+  - class: File
+    location: ../loadContents/inp-filelist.txt
+  - class: Directory
+    location: ../testdir
+inputs: []
+outputs:
+  filelist:
+    type: File
+    outputBinding:
+      glob: inp-filelist.txt
+  testdir:
+    type: Directory
+    outputBinding:
+      glob: testdir
+baseCommand: "true"
diff --git a/tests/iwd/iwd-fileobjs2_noiwdr.cwl b/tests/iwd/iwd-fileobjs2_noiwdr.cwl
new file mode 100644
index 0000000..6aef62b
--- /dev/null
+++ b/tests/iwd/iwd-fileobjs2_noiwdr.cwl
@@ -0,0 +1,18 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+doc: Can have a file declared directly in initialWorkDir
+initialWorkDir:
+  - [{class: File, location: ../loadContents/inp-filelist.txt},
+     {class: Directory, location: ../testdir}]
+inputs: []
+outputs:
+  filelist:
+    type: File
+    outputBinding:
+      glob: inp-filelist.txt
+  testdir:
+    type: Directory
+    outputBinding:
+      glob: testdir
+baseCommand: "true"
diff --git a/tests/iwd/iwd-jsondump1-nl_noiwdr.cwl b/tests/iwd/iwd-jsondump1-nl_noiwdr.cwl
new file mode 100644
index 0000000..68d1596
--- /dev/null
+++ b/tests/iwd/iwd-jsondump1-nl_noiwdr.cwl
@@ -0,0 +1,22 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+initialWorkDir:
+  - entryname: "out-filelist.json"
+    entry: |
+      ${
+        var ls = [];
+        for (var i = 1; i < 10000; i++) {
+          ls.push("example_input_file"+i+".txt");
+        }
+        return ls;
+      }
+requirements:
+  InlineJavascriptRequirement: {}
+inputs: []
+outputs:
+  filelist:
+    type: File
+    outputBinding:
+      glob: out-filelist.json
+arguments: ["true"]
diff --git a/tests/iwd/iwd-jsondump1_noiwdr.cwl b/tests/iwd/iwd-jsondump1_noiwdr.cwl
new file mode 100644
index 0000000..c0e560b
--- /dev/null
+++ b/tests/iwd/iwd-jsondump1_noiwdr.cwl
@@ -0,0 +1,23 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+requirements:
+  InlineJavascriptRequirement: {}
+
+initialWorkDir:
+  - entryname: "out-filelist.json"
+    entry: |-
+      ${
+        var ls = [];
+        for (var i = 1; i < 10000; i++) {
+          ls.push("example_input_file"+i+".txt");
+        }
+        return ls;
+      }
+inputs: []
+outputs:
+  filelist:
+    type: File
+    outputBinding:
+      glob: out-filelist.json
+arguments: ["true"]
diff --git a/tests/iwd/iwd-jsondump2-nl_noiwdr.cwl b/tests/iwd/iwd-jsondump2-nl_noiwdr.cwl
new file mode 100644
index 0000000..b69800c
--- /dev/null
+++ b/tests/iwd/iwd-jsondump2-nl_noiwdr.cwl
@@ -0,0 +1,23 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+requirements:
+  InlineJavascriptRequirement: {}
+
+initialWorkDir:
+  - entryname: "out-filelist.json"
+    entry: |
+      ${
+        var ls = [];
+        for (var i = 1; i < 10000; i++) {
+          ls.push("example_input_file"+i+".txt");
+        }
+        return {"filelist": ls};
+      }
+inputs: []
+outputs:
+  filelist:
+    type: File
+    outputBinding:
+      glob: out-filelist.json
+arguments: ["true"]
diff --git a/tests/iwd/iwd-jsondump2_noiwdr.cwl b/tests/iwd/iwd-jsondump2_noiwdr.cwl
new file mode 100644
index 0000000..84d7220
--- /dev/null
+++ b/tests/iwd/iwd-jsondump2_noiwdr.cwl
@@ -0,0 +1,23 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+requirements:
+  InlineJavascriptRequirement: {}
+
+initialWorkDir:
+  - entryname: "out-filelist.json"
+    entry: |-
+      ${
+        var ls = [];
+        for (var i = 1; i < 10000; i++) {
+          ls.push("example_input_file"+i+".txt");
+        }
+        return {"filelist": ls};
+      }
+inputs: []
+outputs:
+  filelist:
+    type: File
+    outputBinding:
+      glob: out-filelist.json
+arguments: ["true"]
diff --git a/tests/iwd/iwd-jsondump3-nl_noiwdr.cwl b/tests/iwd/iwd-jsondump3-nl_noiwdr.cwl
new file mode 100644
index 0000000..4d92a00
--- /dev/null
+++ b/tests/iwd/iwd-jsondump3-nl_noiwdr.cwl
@@ -0,0 +1,19 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+requirements:
+  InlineJavascriptRequirement: {}
+
+initialWorkDir:
+  - entryname: "out-number.json"
+    entry: |
+      ${
+        return 44.4;
+      }
+inputs: []
+outputs:
+  filelist:
+    type: File
+    outputBinding:
+      glob: out-number.json
+arguments: ["true"]
diff --git a/tests/iwd/iwd-jsondump3_noiwdr.cwl b/tests/iwd/iwd-jsondump3_noiwdr.cwl
new file mode 100644
index 0000000..24a679b
--- /dev/null
+++ b/tests/iwd/iwd-jsondump3_noiwdr.cwl
@@ -0,0 +1,19 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+requirements:
+  InlineJavascriptRequirement: {}
+
+initialWorkDir:
+  - entryname: "out-number.json"
+    entry: |-
+      ${
+        return 44.4;
+      }
+inputs: []
+outputs:
+  filelist:
+    type: File
+    outputBinding:
+      glob: out-number.json
+arguments: ["true"]
diff --git a/tests/iwd/iwd-nolimit_noiwdr.cwl b/tests/iwd/iwd-nolimit_noiwdr.cwl
new file mode 100644
index 0000000..0394af1
--- /dev/null
+++ b/tests/iwd/iwd-nolimit_noiwdr.cwl
@@ -0,0 +1,24 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+requirements:
+  InlineJavascriptRequirement: {}
+
+
+initialWorkDir:
+  - entryname: "out-filelist.txt"
+    entry: |-
+      ${
+        var ls = "";
+        for (var i = 1; i < 10000; i++) {
+          ls += "example_input_file"+i+".txt\n";
+        }
+        return ls;
+      }
+inputs: []
+outputs:
+  filelist:
+    type: File
+    outputBinding:
+      glob: out-filelist.txt
+baseCommand: "true"
diff --git a/tests/iwd/iwd-passthrough1_noreq.cwl b/tests/iwd/iwd-passthrough1_noreq.cwl
new file mode 100644
index 0000000..1a9c0b1
--- /dev/null
+++ b/tests/iwd/iwd-passthrough1_noreq.cwl
@@ -0,0 +1,22 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+doc: |
+  YAML |- syntax does not add trailing newline so in the listing entry
+  below there is no whitespace surrounding the value
+  $(inputs.filelist), so it is evaluated as a File object.  Compare to
+  iwd-passthrough2.cwl
+
+initialWorkDir:
+  - entryname: "renamed-filelist.txt"
+    entry: |-
+      $(inputs.filelist)
+inputs:
+  filelist:
+    type: File
+outputs:
+  filelist:
+    type: File
+    outputBinding:
+      glob: renamed-filelist.txt
+baseCommand: "true"
diff --git a/tests/iwd/iwd-passthrough2_noiwdr.cwl b/tests/iwd/iwd-passthrough2_noiwdr.cwl
new file mode 100644
index 0000000..4b9653c
--- /dev/null
+++ b/tests/iwd/iwd-passthrough2_noiwdr.cwl
@@ -0,0 +1,29 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+doc: |
+  YAML | syntax adds a trailing newline, so in the listing entry
+  below, it becomes a string interpolation -- it evaluates to a string
+  consisting of $(inputs.filelist) serialized to JSON and then adding
+  a newline.  Compare to iwd-passthrough1.cwl
+
+requirements:
+  DockerRequirement:
+    dockerPull: docker.io/python:3-slim
+
+initialWorkDir:
+  - entryname: "renamed-filelist.txt"
+    entry: |
+      $(inputs.filelist)
+
+inputs:
+  filelist: File
+  script:
+    type: File
+    default:
+      class: File
+      location: loadit.py
+stdout: out.txt
+outputs:
+  out: stdout
+arguments: [python3, $(inputs.script), "renamed-filelist.txt"]
diff --git a/tests/iwd/iwd-passthrough3_noreq.cwl b/tests/iwd/iwd-passthrough3_noreq.cwl
new file mode 100644
index 0000000..9997859
--- /dev/null
+++ b/tests/iwd/iwd-passthrough3_noreq.cwl
@@ -0,0 +1,15 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+initialWorkDir:
+  - entryname: "renamed-filelist.txt"
+    entry: $(inputs.filelist)
+inputs:
+  filelist:
+    type: File
+outputs:
+  filelist:
+    type: File
+    outputBinding:
+      glob: renamed-filelist.txt
+baseCommand: "true"
diff --git a/tests/iwd/iwd-passthrough4_noreq.cwl b/tests/iwd/iwd-passthrough4_noreq.cwl
new file mode 100644
index 0000000..7fff53f
--- /dev/null
+++ b/tests/iwd/iwd-passthrough4_noreq.cwl
@@ -0,0 +1,14 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+initialWorkDir:
+  - $(inputs.filelist)
+inputs:
+  filelist:
+    type: File
+outputs:
+  filelist:
+    type: File
+    outputBinding:
+      glob: $(inputs.filelist.basename)
+baseCommand: "true"
diff --git a/tests/iwd/iwd-passthrough5_noreq.cwl b/tests/iwd/iwd-passthrough5_noreq.cwl
new file mode 100644
index 0000000..2ac858f
--- /dev/null
+++ b/tests/iwd/iwd-passthrough5_noreq.cwl
@@ -0,0 +1,15 @@
+class: CommandLineTool
+cwlVersion: v1.2
+doc: Given a directory, emit it unchanged
+initialWorkDir:
+  - entry: $(inputs.testdir)
+    writable: false
+inputs:
+  testdir:
+    type: Directory
+outputs:
+  testdir:
+    type: Directory
+    outputBinding:
+      glob: $(inputs.testdir.basename)
+baseCommand: "true"
diff --git a/tests/iwd/iwd-subdir-tool_noreq.cwl b/tests/iwd/iwd-subdir-tool_noreq.cwl
new file mode 100644
index 0000000..819ce5f
--- /dev/null
+++ b/tests/iwd/iwd-subdir-tool_noreq.cwl
@@ -0,0 +1,15 @@
+class: CommandLineTool
+cwlVersion: v1.2
+doc: Given an input directory, emit a subdirectory as output
+initialWorkDir:
+  - entry: $(inputs.testdir)
+    writable: false
+inputs:
+  testdir:
+    type: Directory
+outputs:
+  testdir:
+    type: Directory
+    outputBinding:
+      glob: testdir/c
+baseCommand: "true"
diff --git a/tests/iwd/iwd-subdir-wf_noreq.cwl b/tests/iwd/iwd-subdir-wf_noreq.cwl
new file mode 100644
index 0000000..a169e51
--- /dev/null
+++ b/tests/iwd/iwd-subdir-wf_noreq.cwl
@@ -0,0 +1,19 @@
+class: Workflow
+cwlVersion: v1.2
+inputs:
+  testdir: Directory
+outputs:
+  out:
+    type: Directory
+    outputSource: step2/testdir
+steps:
+  step1:
+    run: iwd-subdir-tool_noreq.cwl
+    in:
+      testdir: testdir
+    out: [testdir]
+  step2:
+    run: iwd-passthrough5_noreq.cwl
+    in:
+      testdir: step1/testdir
+    out: [testdir]
diff --git a/tests/iwd/iwd_dir_literal_real_file.cwl b/tests/iwd/iwd_dir_literal_real_file.cwl
new file mode 100644
index 0000000..27458e7
--- /dev/null
+++ b/tests/iwd/iwd_dir_literal_real_file.cwl
@@ -0,0 +1,25 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+
+requirements:
+  DockerRequirement:
+      dockerPull: docker.io/debian:stable-slim
+  InlineJavascriptRequirement: {}
+
+initialWorkDir: |
+  ${
+     return [{"class": "Directory",
+              "basename": "subdir",
+              "listing": [ inputs.filelist ]
+              }]}
+
+inputs:
+  filelist: File
+
+outputs:
+  same:
+   type: File
+   outputBinding:
+     glob: subdir/$(inputs.filelist.basename)
+
+baseCommand: echo
diff --git a/tests/iwd/test-index.yaml b/tests/iwd/test-index.yaml
index 68eface..7a4d58b 100644
--- a/tests/iwd/test-index.yaml
+++ b/tests/iwd/test-index.yaml
@@ -391,4 +391,325 @@
       }
     ]
   doc: "Test creation of literal files in the listing"
-  tags: [ initial_work_dir, command_line_tool ]
\ No newline at end of file
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: ../loadContents/input.yml
+  id: iwd-container-entryname1_noreq
+  tool: iwd-container-entryname1_noiwdr.cwl
+  output:
+    "head": {
+        "location": "head.txt",
+        "basename": "head.txt",
+        "class": "File",
+        "checksum": "sha1$8b5071fa49953fcdb8729b16345b7c894b493f83",
+        "size": 241
+    }
+  doc: "Test input mount locations when container required"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: ../loadContents/input.yml
+  id: iwd-container-entryname2_noreq
+  tool: iwd-container-entryname2_noiwdr.cwl
+  should_fail: true
+  doc: "Test initialWorkDir input mount locations when no container (should fail)"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: ../loadContents/input.yml
+  id: iwd-container-entryname3_noreq
+  tool: iwd-container-entryname3_noiwdr.cwl
+  should_fail: true
+  doc: "Test initialWorkDir input mount locations when container is a hint (should fail)"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: ../loadContents/input.yml
+  id: iwd-container-entryname4_noreq
+  tool: iwd-container-entryname4_noiwdr.cwl
+  should_fail: true
+  doc: "Must fail if initialWorkDir.entryname starts with ../"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: null
+  id: iwd-fileobjs1_noreq
+  tool: iwd-fileobjs1_noiwdr.cwl
+  output:
+    "filelist": {
+        "location": "inp-filelist.txt",
+        "basename": "inp-filelist.txt",
+        "class": "File",
+        "checksum": "sha1$57f77b36009332d236b52b4beca77301b503b27c",
+        "size": 268866,
+    }
+    "testdir": {
+        "location": "testdir",
+        "basename": "testdir",
+        "class": "Directory",
+        "listing": [
+            {
+                "class": "File",
+                "location": "b",
+                "basename": "b",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "size": 0,
+            },
+            {
+                "class": "Directory",
+                "location": "c",
+                "basename": "c",
+                "listing": [
+                    {
+                        "class": "File",
+                        "location": "d",
+                        "basename": "d",
+                        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                        "size": 0,
+                    }
+                ],
+            },
+            {
+                "class": "File",
+                "location": "a",
+                "basename": "a",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "size": 0,
+            }
+        ],
+    }
+  doc: "Test File and Directory object in initialWorkDir"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: null
+  id: iwd-fileobjs2_noreq
+  tool: iwd-fileobjs2_noiwdr.cwl
+  output:
+    "filelist": {
+        "location": "inp-filelist.txt",
+        "basename": "inp-filelist.txt",
+        "class": "File",
+        "checksum": "sha1$57f77b36009332d236b52b4beca77301b503b27c",
+        "size": 268866,
+    }
+    "testdir": {
+        "location": "testdir",
+        "basename": "testdir",
+        "class": "Directory",
+        "listing": [
+            {
+                "class": "File",
+                "location": "b",
+                "basename": "b",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "size": 0,
+            },
+            {
+                "class": "Directory",
+                "location": "c",
+                "basename": "c",
+                "listing": [
+                    {
+                        "class": "File",
+                        "location": "d",
+                        "basename": "d",
+                        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                        "size": 0,
+                    }
+                ],
+            },
+            {
+                "class": "File",
+                "location": "a",
+                "basename": "a",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "size": 0,
+            }
+        ],
+    }
+  doc: "Test File and Directory object in initialWorkDir"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: null
+  id: iwd-jsondump1_noreq
+  tool: iwd-jsondump1_noiwdr.cwl
+  output:
+    "filelist": {
+        "location": "out-filelist.json",
+        "basename": "out-filelist.json",
+        "class": "File",
+        "checksum": "sha1$5bbeb2a75327927cb97d7e9716c8299682001b36",
+        "size": 298863
+    }
+  doc: "Test dump object to JSON in initialWorkDir file contents, no trailing newline"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: null
+  id: iwd-jsondump1-nl_noreq
+  tool: iwd-jsondump1-nl_noiwdr.cwl
+  output:
+    "filelist": {
+        "location": "out-filelist.json",
+        "basename": "out-filelist.json",
+        "class": "File",
+        "checksum": "sha1$7307f027449371b3642c1f7c32124218af0e41b5",
+        "size": 298864
+    }
+  doc: "Test dump object to JSON in initialWorkDir file contents, with trailing newline"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: null
+  id: iwd-jsondump2-noreq
+  tool: iwd-jsondump2_noiwdr.cwl
+  output:
+    "filelist": {
+        "location": "out-filelist.json",
+        "basename": "out-filelist.json",
+        "class": "File",
+        "checksum": "sha1$a0e2225d47c9ed2f07e7633d00dd19d1cbf65c9f",
+        "size": 298877,
+    }
+  doc: "Test array to JSON in initialWorkDir file contents, no trailing newline"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: null
+  id: iwd-jsondump2-nl-noreq
+  tool: iwd-jsondump2-nl_noiwdr.cwl
+  output:
+    "filelist": {
+        "location": "out-filelist.json",
+        "basename": "out-filelist.json",
+        "class": "File",
+        "checksum": "sha1$750c95cb45561cd1d863506f82a1a75fffd53a54",
+        "size": 298878,
+    }
+  doc: "Test array to JSON in initialWorkDir file contents, with trailing newline"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: null
+  id: iwd-jsondump3-noreq
+  tool: iwd-jsondump3_noiwdr.cwl
+  output:
+    "filelist": {
+        "location": "out-number.json",
+        "basename": "out-number.json",
+        "class": "File",
+        "checksum": "sha1$356b190d3274c960b34c2c9538023dda438d67d4",
+        "size": 4,
+    }
+  doc: "Test number to JSON in initialWorkDir file contents, no trailing newline"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: null
+  id: iwd-jsondump3-nl-noreq
+  tool: iwd-jsondump3-nl_noiwdr.cwl
+  output:
+    "filelist": {
+        "location": "out-number.json",
+        "basename": "out-number.json",
+        "class": "File",
+        "checksum": "sha1$0b02e6b07d199025bfdcfc6b9830d550a0a6bde9",
+        "size": 5,
+    }
+  doc: "Test number to JSON in initialWorkDir file contents, with trailing newline"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: null
+  id: iwd-nolimit-noreq
+  tool: iwd-nolimit_noiwdr.cwl
+  output:
+   "filelist": {
+        "location": "out-filelist.txt",
+        "basename": "out-filelist.txt",
+        "class": "File",
+        "checksum": "sha1$57f77b36009332d236b52b4beca77301b503b27c",
+        "size": 268866,
+    }
+  doc: "Test that initialWorkDir contents can be bigger than 64k"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: ../loadContents/input.yml
+  id: iwd-passthrough1-noreq
+  tool: iwd-passthrough1_noreq.cwl
+  output:
+    "filelist": {
+        "location": "renamed-filelist.txt",
+        "basename": "renamed-filelist.txt",
+        "class": "File",
+        "checksum": "sha1$57f77b36009332d236b52b4beca77301b503b27c",
+        "size": 268866,
+    }
+  doc: "Test initialWorkDir file passthrough"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: ../loadContents/input.yml
+  id: iwd-passthrough2-noreq
+  tool: iwd-passthrough2_noiwdr.cwl
+  output:
+    "out": {
+        "location": "out.txt",
+        "basename": "out.txt",
+        "class": "File",
+        "checksum": "sha1$406e83b1cd694780f1b3ea4fe8fbb754511fe3f7",
+        "size": 49,
+    }
+  doc: "Test initialWorkDir file object is serialized to json"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: ../loadContents/input.yml
+  id: iwd-passthrough3-noreq
+  tool: iwd-passthrough3_noreq.cwl
+  output:
+    "filelist": {
+        "location": "renamed-filelist.txt",
+        "basename": "renamed-filelist.txt",
+        "class": "File",
+        "checksum": "sha1$57f77b36009332d236b52b4beca77301b503b27c",
+        "size": 268866,
+    }
+  doc: "Test initialWorkDir file object is passed through"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: ../loadContents/input.yml
+  id: iwd-passthrough4-noreq
+  tool: iwd-passthrough4_noreq.cwl
+  output:
+    "filelist": {
+        "location": "inp-filelist.txt",
+        "basename": "inp-filelist.txt",
+        "class": "File",
+        "checksum": "sha1$57f77b36009332d236b52b4beca77301b503b27c",
+        "size": 268866,
+    }
+  doc: "Test initialWorkDir file object is passed through"
+  tags: [ initial_work_dir, command_line_tool ]
+
+- job: iwd-subdir-job.yml
+  id: iwd-subdir-noreq
+  tool: iwd-subdir-wf_noreq.cwl
+  doc: "Test emitting a subdirectory from initialWorkDir"
+  output:
+    "out": {
+        "location": "c",
+        "basename": "c",
+        "class": "Directory",
+        "listing": [
+            {
+                "location": "d",
+                "basename": "d",
+                "class": "File",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "size": 0
+            }
+        ]
+    }
+  tags: [ initial_work_dir, command_line_tool, workflow ]
+
+- job: ../loadContents/input.yml
+  id: iwd_dir_literal_real_file
+  tool: iwd_dir_literal_real_file.cwl
+  doc: "Test initialWorkDir directory literal containing a real file"
+  output:
+    same:
+      "location": "inp-filelist.txt"
+      "basename": "inp-filelist.txt"
+      "class": "File"
+      "checksum": "sha1$57f77b36009332d236b52b4beca77301b503b27c"
+      "size": 268866
+  tags: [ initial_work_dir, command_line_tool ]
diff --git a/tests/iwdr-entry_noreq.cwl b/tests/iwdr-entry_noreq.cwl
new file mode 100644
index 0000000..6895789
--- /dev/null
+++ b/tests/iwdr-entry_noreq.cwl
@@ -0,0 +1,18 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+baseCommand: ["cat", "example.conf"]
+
+initialWorkDir:
+  - entryname: example.conf
+    entry: |
+      CONFIGVAR=$(inputs.message)
+
+inputs:
+  message: string
+outputs:
+  out:
+    type: File
+    outputBinding:
+      glob: example.conf
diff --git a/tests/iwdr_with_nested_dirs_noreq.cwl b/tests/iwdr_with_nested_dirs_noreq.cwl
new file mode 100644
index 0000000..24cd769
--- /dev/null
+++ b/tests/iwdr_with_nested_dirs_noreq.cwl
@@ -0,0 +1,39 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.3.0-dev1
+class: Workflow
+
+inputs: []
+outputs:
+  ya_empty:
+    type: File
+    outputSource: second/ya
+
+steps:
+  first:
+    run:
+      class: CommandLineTool
+      baseCommand: [ mkdir, -p, deeply/nested/dir/structure ]
+      inputs: []
+      outputs:
+        deep_dir:
+          type: Directory
+          outputBinding: { glob: deeply }
+    in: {}
+    out: [ deep_dir ]
+
+  second:
+    run:
+      class: CommandLineTool
+      baseCommand: [ touch, deeply/nested/dir/structure/ya ]
+      initialWorkDir:
+        - entry: $(inputs.dir)
+          writable: true
+      inputs:
+        dir: Directory
+      outputs:
+        ya:
+          type: File
+          outputBinding: { glob: deeply/nested/dir/structure/ya }
+
+    in: { dir: first/deep_dir }
+    out: [ ya ]
diff --git a/tests/linkfile_noreq.cwl b/tests/linkfile_noreq.cwl
new file mode 100644
index 0000000..78e868b
--- /dev/null
+++ b/tests/linkfile_noreq.cwl
@@ -0,0 +1,20 @@
+cwlVersion: v1.3.0-dev1
+class: CommandLineTool
+
+initialWorkDir:
+  - $(inputs.src)
+
+inputs:
+  src:
+    type: File
+    inputBinding:
+      position: 1
+      valueFrom: $(self.nameroot).class
+
+baseCommand: touch
+
+outputs:
+  classfile:
+    type: File
+    outputBinding:
+      glob: "*.class"
diff --git a/tests/networkaccess_noreq.cwl b/tests/networkaccess_noreq.cwl
new file mode 100644
index 0000000..0cc14b5
--- /dev/null
+++ b/tests/networkaccess_noreq.cwl
@@ -0,0 +1,14 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+requirements:
+  DockerRequirement:
+    dockerPull: docker.io/python:3-slim
+networkAccess: true
+inputs: []
+outputs: []
+baseCommand: python
+arguments:
+  - "-c"
+  - valueFrom: |
+      import urllib.request
+      assert(urllib.request.urlopen("http://commonwl.org").code == 200)
diff --git a/tests/recursive-input-directory_noiwdr.cwl b/tests/recursive-input-directory_noiwdr.cwl
new file mode 100644
index 0000000..db74ddb
--- /dev/null
+++ b/tests/recursive-input-directory_noiwdr.cwl
@@ -0,0 +1,33 @@
+cwlVersion: v1.3.0-dev1
+class: CommandLineTool
+requirements:
+  ShellCommandRequirement: {}
+
+initialWorkDir:
+  - entry: $(inputs.input_dir)
+    entryname: work_dir
+    writable: true
+stdout: output.txt
+arguments:
+ - shellQuote: false
+   valueFrom: |
+    touch work_dir/e;
+    if [ ! -w work_dir ]; then echo work_dir not writable; fi;
+    if [ -L work_dir ]; then echo work_dir is a symlink; fi;
+    if [ ! -w work_dir/a ]; then echo work_dir/a not writable; fi;
+    if [ -L work_dir/a ]; then echo work_dir/a is a symlink; fi;
+    if [ ! -w work_dir/c ]; then echo work_dir/c not writable; fi;
+    if [ -L work_dir/c ]; then echo work_dir/c is a symlink; fi;
+    if [ ! -w work_dir/c/d ]; then echo work_dir/c/d not writable; fi;
+    if [ -L work_dir/c/d ]; then echo work_dir/c/d is a symlink; fi;
+    if [ ! -w work_dir/e ]; then echo work_dir/e not writable; fi;
+    if [ -L work_dir/e ]; then echo work_dir/e is a symlink ; fi;
+inputs:
+  input_dir: Directory
+outputs:
+  output_dir:
+    type: Directory
+    outputBinding:
+      glob: work_dir
+  test_result:
+    type: stdout
diff --git a/tests/rename_noreq.cwl b/tests/rename_noreq.cwl
new file mode 100644
index 0000000..99deb2d
--- /dev/null
+++ b/tests/rename_noreq.cwl
@@ -0,0 +1,14 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+baseCommand: "true"
+initialWorkDir:
+  - entryname: $(inputs.newname)
+    entry: $(inputs.srcfile)
+inputs:
+  srcfile: File
+  newname: string
+outputs:
+  outfile:
+    type: File
+    outputBinding:
+      glob: $(inputs.newname)
diff --git a/tests/search_noiwdr.cwl b/tests/search_noiwdr.cwl
new file mode 100644
index 0000000..910081f
--- /dev/null
+++ b/tests/search_noiwdr.cwl
@@ -0,0 +1,109 @@
+cwlVersion: v1.3.0-dev1
+$graph:
+- id: index
+  class: CommandLineTool
+  baseCommand: python
+  arguments:
+    - valueFrom: input.txt
+      position: 1
+  initialWorkDir:
+    - entryname: input.txt
+      entry: $(inputs.file)
+  requirements:
+    - class: InlineJavascriptRequirement
+  hints:
+    - class: DockerRequirement
+      dockerPull: docker.io/python:3-slim
+
+  inputs:
+    file:  File
+    secondfile:  File
+    index.py:
+      type: File
+      default:
+        class: File
+        location: index.py
+      inputBinding:
+        position: 0
+  outputs:
+    result:
+      type: File
+      outputBinding:
+        glob: input.txt
+      secondaryFiles:
+        - ".idx1"
+        - "^.idx2"
+        - '$(self.basename).idx3'
+        - '${ return self.basename+".idx4"; }'
+        - '$({"path": self.path+".idx5", "class": "File"})'
+        - '$(self.nameroot).idx6$(self.nameext)'
+        - '${ return [self.basename+".idx7", inputs.secondfile]; }'
+        - "_idx8"
+
+- id: search
+  class: CommandLineTool
+  baseCommand: python
+  requirements:
+    - class: InlineJavascriptRequirement
+  hints:
+    - class: DockerRequirement
+      dockerPull: docker.io/python:3-slim
+  inputs:
+    file:
+      type: File
+      inputBinding:
+        position: 1
+      secondaryFiles:
+        - ".idx1"
+        - "^.idx2"
+        - '$(self.basename).idx3'
+        - '${ return self.basename+".idx4"; }'
+        - '$(self.nameroot).idx6$(self.nameext)'
+        - '${ return [self.basename+".idx7"]; }'
+        - "_idx8"
+    search.py:
+      type: File
+      default:
+        class: File
+        location: search.py
+      inputBinding:
+        position: 0
+    term:
+      type: string
+      inputBinding:
+        position: 2
+  outputs:
+    result:
+      type: File
+      outputBinding:
+        glob: result.txt
+  stdout: result.txt
+
+- id: main
+  class: Workflow
+  inputs:
+    infile: File
+    secondfile: File
+    term: string
+  outputs:
+    outfile:
+      type: File
+      outputSource: search/result
+    indexedfile:
+      type: File
+      outputSource: index/result
+
+  steps:
+    index:
+      run: "#index"
+      in:
+        file: infile
+        secondfile: secondfile
+      out: [result]
+
+    search:
+      run: "#search"
+      in:
+        file: index/result
+        term: term
+      out: [result]
diff --git a/tests/secondaryfiles/rename-outputs_noiwdr.cwl b/tests/secondaryfiles/rename-outputs_noiwdr.cwl
new file mode 100644
index 0000000..c11191e
--- /dev/null
+++ b/tests/secondaryfiles/rename-outputs_noiwdr.cwl
@@ -0,0 +1,49 @@
+#!/usr/bin/env cwl-runner
+id: OutputSecondaryFileConformanceTest
+baseCommand:
+- ls
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+doc: |
+  Simple test to confirm the implementation of expressions returning a File within a CommandOutputParameter.secondaryFile field.
+
+  Related links:
+  - Issue: https://github.com/common-workflow-language/cwltool/issues/1232
+  - PR: https://github.com/common-workflow-language/cwltool/pull/1233
+  - Discourse: https://cwl.discourse.group/t/ask-cwl-to-rename-a-secondary-file/72
+
+inputs: []
+outputs:
+- id: output_file
+  label: out
+  outputBinding:
+    glob: "*.txt"
+  secondaryFiles: |
+   ${
+        function resolveSecondary(base, secPattern) {
+          if (secPattern[0] == "^") {
+            var spl = base.split(".");
+            var endIndex = spl.length > 1 ? spl.length - 1 : 1;
+            return resolveSecondary(spl.slice(undefined, endIndex).join("."), secPattern.slice(1));
+          }
+          return base + secPattern;
+        }
+        return [
+          {
+            "class": "File",
+            "path": resolveSecondary(self.path, "^.accessory"),
+            "basename": resolveSecondary(self.basename, ".accessory")
+          }
+        ];
+   }
+  type: File
+requirements:
+  InlineJavascriptRequirement: {}
+
+initialWorkDir:
+  - entry: ""
+    entryname: secondary_file_test.txt
+    writable: true
+  - entry: ""
+    entryname: secondary_file_test.accessory
+    writable: true
diff --git a/tests/secondaryfiles/test-index.yaml b/tests/secondaryfiles/test-index.yaml
index 54fb40e..f540dfe 100644
--- a/tests/secondaryfiles/test-index.yaml
+++ b/tests/secondaryfiles/test-index.yaml
@@ -11,7 +11,7 @@
   tags: [ inline_javascript, secondary_files, command_line_tool, shell_command ]
 
 - tool: rename-outputs.cwl
-  doc: Confirm CommandOutputParameter expression can receive a File object
+  doc: Confirm CommandOutputParameter expression can receive a File object (using InitialWorkDirRequirement)
   id: command_output_file_expression
   output:
     output_file:
@@ -24,4 +24,20 @@
         checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
         location: secondary_file_test.txt.accessory
         size: 0
-  tags: [ inline_javascript, secondary_files, command_line_tool ]
+  tags: [ inline_javascript, secondary_files, command_line_tool, initial_work_dir]
+
+- tool: rename-outputs_noiwdr.cwl
+  doc: Confirm CommandOutputParameter expression can receive a File object (using initialWorkDir)
+  id: command_output_file_expression_noiwdr
+  output:
+    output_file:
+      class: File
+      checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
+      size: 0
+      location: secondary_file_test.txt
+      secondaryFiles:
+      - class: File
+        checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
+        location: secondary_file_test.txt.accessory
+        size: 0
+  tags: [ inline_javascript, secondary_files, command_line_tool, initial_work_dir ]
diff --git a/tests/stage-array-dirs_noreq.cwl b/tests/stage-array-dirs_noreq.cwl
new file mode 100644
index 0000000..9c59459
--- /dev/null
+++ b/tests/stage-array-dirs_noreq.cwl
@@ -0,0 +1,20 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+id: stage_array_dirs
+baseCommand:
+  - ls
+inputs:
+  - id: input_list
+    type: Directory[]
+outputs:
+  - id: output
+    type: File[]
+    outputBinding:
+      glob:
+      - testdir/a
+      - rec/B
+label: stage-array-dirs.cwl
+initialWorkDir:
+  - $(inputs.input_list)
diff --git a/tests/stage-array_noiwdr.cwl b/tests/stage-array_noiwdr.cwl
new file mode 100644
index 0000000..544d147
--- /dev/null
+++ b/tests/stage-array_noiwdr.cwl
@@ -0,0 +1,32 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+id: stage_array
+arguments:
+  - {shellQuote: false, valueFrom: "ls | grep -v lsout"}
+inputs:
+  - id: input_file
+    type: File
+  - id: optional_file
+    type: File?
+  - id: input_list
+    type: 'File[]'
+    secondaryFiles:
+      - ^.tar
+stdout: lsout
+outputs:
+  - id: output
+    type: File?
+    outputBinding:
+      glob: lsout
+label: stage-array.cwl
+initialWorkDir:
+  - $(inputs.input_file)
+  - $(inputs.optional_file)
+  - entry: $(inputs.input_list)
+  - entry: $(null)
+  - entryname: a
+    entry: b
+requirements:
+  - class: ShellCommandRequirement
diff --git a/tests/stage_file_array_basename_and_entryname_noiwdr.cwl b/tests/stage_file_array_basename_and_entryname_noiwdr.cwl
new file mode 100644
index 0000000..8882b3b
--- /dev/null
+++ b/tests/stage_file_array_basename_and_entryname_noiwdr.cwl
@@ -0,0 +1,23 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+id: stage_file_array_basename_and_entryname
+label: Stage File Array (with Directory Basename AND entryname)
+arguments: [ls]
+inputs:
+  - id: input_list
+    type: 'File[]'
+    secondaryFiles:
+      - .sec
+outputs:
+  - id: output
+    type: File[]
+    outputBinding:
+      glob: input_dir/*
+requirements:
+  - class: InlineJavascriptRequirement
+
+initialWorkDir:
+  - entryname: input_dir
+    entry: "${ return {class: 'Directory', basename: 'not_input_dir', listing: inputs.input_list} }"
diff --git a/tests/stage_file_array_noiwdr.cwl b/tests/stage_file_array_noiwdr.cwl
new file mode 100644
index 0000000..6aaadfa
--- /dev/null
+++ b/tests/stage_file_array_noiwdr.cwl
@@ -0,0 +1,23 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+id: stage_file_array
+label: Stage File Array
+arguments: [ls]
+inputs:
+  - id: input_list
+    type: 'File[]'
+    secondaryFiles:
+      - .sec
+outputs:
+  - id: output
+    type: File[]
+    outputBinding:
+      glob: input_dir/*
+requirements:
+  - class: InlineJavascriptRequirement
+
+initialWorkDir:
+  - entryname: input_dir
+    entry: "${ return {class: 'Directory', listing: inputs.input_list} }"
diff --git a/tests/stagefile_noreq.cwl b/tests/stagefile_noreq.cwl
new file mode 100644
index 0000000..0256d29
--- /dev/null
+++ b/tests/stagefile_noreq.cwl
@@ -0,0 +1,25 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+hints:
+  - class: DockerRequirement
+    dockerPull: docker.io/python:3-slim
+
+initialWorkDir:
+  - entry: $(inputs.infile)
+    entryname: bob.txt
+    writable: true
+inputs:
+  infile: File
+outputs:
+  outfile:
+    type: File
+    outputBinding:
+      glob: bob.txt
+baseCommand: "python"
+arguments:
+  - "-c"
+  - |
+    f = open("bob.txt", "r+")
+    f.seek(8)
+    f.write("Bob.    ")
+    f.close()
diff --git a/tests/string-interpolation/bash-dollar-quote_noiwdr.cwl b/tests/string-interpolation/bash-dollar-quote_noiwdr.cwl
new file mode 100644
index 0000000..aaeedf9
--- /dev/null
+++ b/tests/string-interpolation/bash-dollar-quote_noiwdr.cwl
@@ -0,0 +1,56 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+requirements:
+  InlineJavascriptRequirement: {}
+
+
+initialWorkDir:
+  - entryname: script.sh
+    entry: |
+      echo \$(echo \
+        "My country, 'tis of thee," \
+        "Sweet land of liberty" | rev)
+      echo '$(inputs.val)'     # produce val
+      echo '\$(inputs.val)'    # produce $(inputs.val)
+      echo
+      echo '\\$(inputs.val)'   # produce \val
+      echo '\\\$(inputs.val)'  # produce \$(inputs.val)
+      echo
+      echo '\\\\$(inputs.val)'  # produce \\val
+      echo '\\\\\$(inputs.val)'  # produce \\$(inputs.val)
+      echo
+      echo '\\\\\\$(inputs.val)'  # produce \\\val
+      echo '\\\\\\\$(inputs.val)'  # produce \\\$(inputs.val)
+      echo
+      echo '\\\\\\\\$(inputs.val)'  # produce \\\\val
+      echo '\\\\\\\\\$(inputs.val)'  # produce \\\\$(inputs.val)
+      echo
+      echo '\\\\\\\\\\$(inputs.val)'  # produce \\\\\val
+      echo '\\\\\\\\\\\$(inputs.val)'  # produce \\\\\$(inputs.val)
+      echo '\'          # produce \
+      echo '\\'         # produce \
+      echo '\\\'        # produce \\
+      echo '\\\\'       # produce \\
+      echo '\\\\\'      # produce \\\
+      echo '\\\\\\'     # produce \\\
+      echo '\\\\\\\'    # produce \\\\
+      echo '\\\\\\\\'   # produce \\\\
+      echo '\\\\\\\\\'  # produce \\\\\
+      echo '\\\\\\\\\\' # produce \\\\\
+      echo '$'          # produce $
+      echo '\$'         # produce \$
+      echo '\\$'        # produce \$
+      echo '$$'         # produce $$
+      echo '$$$'        # produce $$$
+
+baseCommand: ["bash", "script.sh"]
+
+inputs:
+  val:
+    type: string
+    default: "val"
+
+outputs:
+  out: stdout
+
+stdout: out.txt
diff --git a/tests/string-interpolation/bash-line-continuation-with-expression_noreq.cwl b/tests/string-interpolation/bash-line-continuation-with-expression_noreq.cwl
new file mode 100644
index 0000000..176a8a0
--- /dev/null
+++ b/tests/string-interpolation/bash-line-continuation-with-expression_noreq.cwl
@@ -0,0 +1,20 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+initialWorkDir:
+  - entryname: script.sh
+    entry: |
+      echo \
+        "My country, 'tis of thee," \
+        "Sweet land of $(inputs.liberty)"
+
+baseCommand: ["bash", "script.sh"]
+
+inputs:
+  liberty:
+    type: string?
+    default: liberty
+
+outputs:
+  out: stdout
+
+stdout: out.txt
diff --git a/tests/string-interpolation/bash-line-continuation_noreq.cwl b/tests/string-interpolation/bash-line-continuation_noreq.cwl
new file mode 100644
index 0000000..13a3bbb
--- /dev/null
+++ b/tests/string-interpolation/bash-line-continuation_noreq.cwl
@@ -0,0 +1,17 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+initialWorkDir:
+  - entryname: script.sh
+    entry: |
+      echo \
+        "My country, 'tis of thee," \
+        "Sweet land of liberty"
+
+baseCommand: ["bash", "script.sh"]
+
+inputs: []
+
+outputs:
+  out: stdout
+
+stdout: out.txt
diff --git a/tests/string-interpolation/js-quote_noiwdr.cwl b/tests/string-interpolation/js-quote_noiwdr.cwl
new file mode 100644
index 0000000..40f75d9
--- /dev/null
+++ b/tests/string-interpolation/js-quote_noiwdr.cwl
@@ -0,0 +1,36 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+label: Check for a JS quoting bug
+
+requirements:
+  InlineJavascriptRequirement: {}
+  ResourceRequirement:
+    coresMin: 2
+    ramMin: 1000
+
+
+initialWorkDir:
+  - entryname: file.txt
+    entry: |
+      ${return 'quote "' + inputs.quote + '"'}
+  - entryname: script.sh
+    entry: |
+      set -xe
+      cat file.txt
+
+inputs:
+  quote:
+    type: string
+    default: Hello
+
+outputs:
+  out:
+    type: File
+    outputBinding:
+      glob: file.txt
+
+baseCommand:
+- echo
+arguments: []
diff --git a/tests/string-interpolation/test-index.yaml b/tests/string-interpolation/test-index.yaml
index cc6e2b3..8607888 100644
--- a/tests/string-interpolation/test-index.yaml
+++ b/tests/string-interpolation/test-index.yaml
@@ -1,7 +1,7 @@
 # Run with cwltest --test test-index.yaml --tool toil-cwl-runner -- --enable-dev
 
 - id: continuation
-  doc: Line continuations in bash scripts should behave correctly
+  doc: Line continuations in bash scripts should behave correctly (using InitialWorkDirRequirement)
   tool: bash-line-continuation.cwl
   output:
     out: {
@@ -10,10 +10,10 @@
         "location": "out.txt",
         "size": 48
     }
-  tags: [ inline_javascript, command_line_tool ]
+  tags: [ inline_javascript, command_line_tool, initial_work_dir ]
 
 - id: continuation_expression
-  doc: Line continuations in bash scripts should always behave correctly
+  doc: Line continuations in bash scripts should always behave correctly (using InitialWorkDirRequirement)
   tool: bash-line-continuation-with-expression.cwl
   output:
     out: {
@@ -22,10 +22,10 @@
         "location": "out.txt",
         "size": 48
     }
-  tags: [ inline_javascript, command_line_tool ]
+  tags: [ inline_javascript, command_line_tool, initial_work_dir ]
 
 - id: quoting_multiple_backslashes
-  doc: Test quoting multiple backslashes
+  doc: Test quoting multiple backslashes using InitialWorkDirRequirement
   tool: bash-dollar-quote.cwl
   output:
     out: {
@@ -34,7 +34,7 @@
         "location": "out.txt",
         "size": 246
     }
-  tags: [ inline_javascript, command_line_tool ]
+  tags: [ inline_javascript, command_line_tool, initial_work_dir ]
 
 - id: escaping_expression_no_extra_quotes
   doc: Strings returned from JS expressions should not have extra quotes around them
@@ -46,4 +46,52 @@
         "location": "file.txt",
         "size": 14
     }
-  tags: [ inline_javascript, command_line_tool ]
+  tags: [ inline_javascript, command_line_tool, initial_work_dir ]
+
+- id: continuation_noiwdr
+  doc: Line continuations in bash scripts should behave correctly (using initialWorkDir)
+  tool: bash-line-continuation_noreq.cwl
+  output:
+    out: {
+        "checksum": "sha1$47d8510dce768c907f4dea6bcaf90f8d59cb265c",
+        "class": "File",
+        "location": "out.txt",
+        "size": 48
+    }
+  tags: [ inline_javascript, command_line_tool, initial_work_dir ]
+
+- id: continuation_expression_noiwdr
+  doc: Line continuations in bash scripts should always behave correctly (using initialWorkDir)
+  tool: bash-line-continuation-with-expression_noreq.cwl
+  output:
+    out: {
+        "checksum": "sha1$47d8510dce768c907f4dea6bcaf90f8d59cb265c",
+        "class": "File",
+        "location": "out.txt",
+        "size": 48
+    }
+  tags: [ inline_javascript, command_line_tool, initial_work_dir ]
+
+- id: quoting_multiple_backslashes_noiwdr
+  doc: Test quoting multiple backslashes using initialWorkDir
+  tool: bash-dollar-quote_noiwdr.cwl
+  output:
+    out: {
+        "checksum": "sha1$acfdc38aef5354c03b976cbb6d9f7d08a179951d",
+        "class": "File",
+        "location": "out.txt",
+        "size": 246
+    }
+  tags: [ inline_javascript, command_line_tool, initial_work_dir ]
+
+- id: escaping_expression_no_extra_quotes_noiwdr
+  doc: Strings returned from JS expressions should not have extra quotes around them (using initialWorkDir)
+  tool: js-quote_noiwdr.cwl
+  output:
+    out: {
+        "checksum": "sha1$726e9e616f278d9028b4a870653b01c125c2fc89",
+        "class": "File",
+        "location": "file.txt",
+        "size": 14
+    }
+  tags: [ inline_javascript, command_line_tool, initial_work_dir ]
diff --git a/tests/template-tool_noiwdr.cwl b/tests/template-tool_noiwdr.cwl
new file mode 100755
index 0000000..9fb94a7
--- /dev/null
+++ b/tests/template-tool_noiwdr.cwl
@@ -0,0 +1,25 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.3.0-dev1
+class: CommandLineTool
+requirements:
+  - class: InlineJavascriptRequirement
+    expressionLib:
+      - { $include: underscore.js }
+      - "var t = function(s) { return _.template(s, {variable: 'data'})({'inputs': inputs}); };"
+
+initialWorkDir:
+  - entryname: foo.txt
+    entry: $(t("The file is <%= data.inputs.file1.path.split('/').slice(-1)[0] %>\n"))
+
+hints:
+  DockerRequirement:
+    dockerPull: docker.io/debian:stable-slim
+inputs:
+  - id: file1
+    type: File
+outputs:
+  - id: foo
+    type: File
+    outputBinding:
+      glob: foo.txt
+baseCommand: [cat, foo.txt]
diff --git a/tests/updatedir_inplace_noiwdr.cwl b/tests/updatedir_inplace_noiwdr.cwl
new file mode 100755
index 0000000..7270c15
--- /dev/null
+++ b/tests/updatedir_inplace_noiwdr.cwl
@@ -0,0 +1,20 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+requirements:
+  InplaceUpdateRequirement:
+    inplaceUpdate: true
+
+initialWorkDir:
+  - entry: $(inputs.r)
+    entryname: inp
+    writable: true
+
+inputs:
+  r: Directory
+outputs:
+  out:
+    type: Directory
+    outputBinding:
+      glob: inp
+arguments: [touch, inp/blurb]
diff --git a/tests/updateval_inplace_noiwdr.cwl b/tests/updateval_inplace_noiwdr.cwl
new file mode 100755
index 0000000..d0c5cfc
--- /dev/null
+++ b/tests/updateval_inplace_noiwdr.cwl
@@ -0,0 +1,27 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+requirements:
+  InplaceUpdateRequirement:
+    inplaceUpdate: true
+
+initialWorkDir:
+  - entry: $(inputs.r)
+    writable: true
+
+hints:
+  DockerRequirement:
+    dockerPull: docker.io/python:3-slim
+inputs:
+  r: File
+  script:
+    type: File
+    default:
+      class: File
+      location: updateval.py
+outputs:
+  out:
+    type: File
+    outputBinding:
+      glob: $(inputs.r.basename)
+arguments: [python, $(inputs.script), $(inputs.r.basename)]
diff --git a/tests/writable-dir-docker_noiwdr.cwl b/tests/writable-dir-docker_noiwdr.cwl
new file mode 100644
index 0000000..4af55cf
--- /dev/null
+++ b/tests/writable-dir-docker_noiwdr.cwl
@@ -0,0 +1,23 @@
+cwlVersion: v1.3.0-dev1
+
+class: CommandLineTool
+
+requirements:
+  - class: InlineJavascriptRequirement
+
+initialWorkDir:
+  - entryname: emptyWritableDir
+    entry: "$({class: 'Directory', listing: []})"
+    writable: true
+
+hints:
+  - class: DockerRequirement
+    dockerPull: docker.io/alpine:latest
+
+inputs: []
+outputs:
+  out:
+    type: Directory
+    outputBinding:
+      glob: emptyWritableDir
+arguments: [touch, emptyWritableDir/blurg]
diff --git a/tests/writable-dir_noiwdr.cwl b/tests/writable-dir_noiwdr.cwl
new file mode 100644
index 0000000..ae6ce7f
--- /dev/null
+++ b/tests/writable-dir_noiwdr.cwl
@@ -0,0 +1,17 @@
+cwlVersion: v1.3.0-dev1
+class: CommandLineTool
+requirements:
+  InlineJavascriptRequirement: {}
+
+initialWorkDir:
+  - entryname: emptyWritableDir
+    writable: true
+    entry: "$({class: 'Directory', listing: []})"
+
+inputs: []
+outputs:
+  out:
+    type: Directory
+    outputBinding:
+      glob: emptyWritableDir
+arguments: [touch, emptyWritableDir/blurg]

From 15cbfa25d5559783862360a493a2e7af616ff7ea Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Fri, 19 Jul 2024 08:41:25 -0400
Subject: [PATCH 6/6] fix typo

---
 .github/config/wordlist.txt | 1 +
 CommandLineTool.yml         | 6 +++---
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/config/wordlist.txt b/.github/config/wordlist.txt
index 30d75d8..69fa165 100644
--- a/.github/config/wordlist.txt
+++ b/.github/config/wordlist.txt
@@ -122,6 +122,7 @@ implementer
 implementers
 implementor
 implementors
+initialworkdir
 initialworkdirrequirement
 initialworkdirrequirements
 inlinejavascriptrequirement
diff --git a/CommandLineTool.yml b/CommandLineTool.yml
index 09cd1d6..31e72af 100644
--- a/CommandLineTool.yml
+++ b/CommandLineTool.yml
@@ -54,14 +54,14 @@ $graph:
       See also the [CWL Workflow Description, v1.3.0-dev1 changelog](Workflow.html#Changelog).
 
       * New field `networkAccess` on
-        [CommandLineTool](#CommandLineTool).  This supercedes the
+        [CommandLineTool](#CommandLineTool).  This supersedes the
         [NetworkAccess](#NetworkAccess) requirement, which is now
         deprecated.
       * New field `envDef` on [CommandLineTool](#CommandLineTool).
-        This supercedes the [EnvVarRequirement](#EnvVarRequirement)
+        This supersedes the [EnvVarRequirement](#EnvVarRequirement)
         requirement, which is now deprecated.
       * New field `initialWorkDir` on
-        [CommandLineTool](#CommandLineTool).  This supercedes the
+        [CommandLineTool](#CommandLineTool).  This supersedes the
         [InitialWorkDirRequirement](#InitialWorkDirRequirement)
         requirement, which is now deprecated.