diff --git a/.github/workflows/cwltool.yml b/.github/workflows/cwltool.yml
index 6a95340..d57ac9b 100644
--- a/.github/workflows/cwltool.yml
+++ b/.github/workflows/cwltool.yml
@@ -21,10 +21,10 @@ jobs:
 
       - uses: actions/setup-python@v6
         with:
-          python-version: '3.9.x'
+          python-version: '3.10.x'
 
       - name: Setup prerequirements
-        run: pip install "cwltest>=2.3" pytest-xdist "cwltool>=3.1.20240909164951"
+        run: pip install "cwltest>=2.3" pytest-xdist git+https://github.com/common-workflow-language/cwltool.git@refs/pull/2177/head
 
       - name: Copy in cwltool-specific configuration for the cwltest pytest plugin
         run: cp "$(python -c 'from cwltool.tests.util import get_data; print(get_data("tests/cwl-conformance/cwltool-conftest.py"))')" conftest.py
diff --git a/CommandLineTool.yml b/CommandLineTool.yml
index 604c668..23b674d 100644
--- a/CommandLineTool.yml
+++ b/CommandLineTool.yml
@@ -51,6 +51,17 @@ $graph:
 
       ## Changelog for v1.3.0-dev1
 
+      * [Output Binding](#Output_binding): Any output present in the
+        "cwl.output.json" file but not declared in the `outputs` section must
+        be discarded from the output object. Previous versions of CWL did not
+        define if undeclared outputs in "cwl.output.json" should be present
+        in the output object.
+
+      ### Updated Conformance Tests for v1.3.0
+
+      * Reduced the usage of `ShellCommandRequirement` in the conformance tests,
+        making several more of the `required`.
+
       See also the [CWL Workflow Description, v1.3.0-dev1 changelog](Workflow.html#Changelog).
       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)
diff --git a/conformance_tests.yaml b/conformance_tests.yaml
index 2cad4f7..0de2c0f 100644
--- a/conformance_tests.yaml
+++ b/conformance_tests.yaml
@@ -109,7 +109,7 @@
       checksum: sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15
       size: 4
       location: error.txt
-  tags: [ shell_command, command_line_tool ]
+  tags: [ required, command_line_tool ]
 
 - job: tests/empty.json
   tool: tests/stderr-shortcut.cwl
@@ -121,7 +121,7 @@
       checksum: sha1$f1d2d2f924e986ac86fdf7b36c94bcdf32beec15
       size: 4
       location: Any
-  tags: [ shell_command, command_line_tool ]
+  tags: [ required, command_line_tool ]
 
 - output:
     output_file:
@@ -133,7 +133,7 @@
   tool: tests/stderr-mediumcut.cwl
   id: stderr_redirect_mediumcut
   doc: Test command line with stderr redirection, named brief syntax
-  tags: [ shell_command, command_line_tool ]
+  tags: [ required, command_line_tool ]
 
 - job: tests/cat-job.json
   output:
@@ -951,7 +951,7 @@
   doc: >-
     Test support for reading cwl.output.json when running in a Docker container
     and just 'path' is provided.
-  tags: [ shell_command, command_line_tool ]
+  tags: [ required, command_line_tool ]
 
 - job: tests/empty.json
   output: {
@@ -1110,7 +1110,7 @@
   tool: tests/dir.cwl
   id: directory_input_param_ref
   doc: Test directory input with parameter reference
-  tags: [ shell_command, command_line_tool ]
+  tags: [ required, command_line_tool ]
 
 - job: tests/dir-job.yml
   output:
@@ -1123,7 +1123,7 @@
   tool: tests/dir2.cwl
   id: directory_input_docker
   doc: Test directory input in Docker
-  tags: [ command_line_tool, shell_command ]
+  tags: [ required, command_line_tool ]
 
 - job: tests/dir3-job.yml
   output:
@@ -1161,7 +1161,7 @@
   tool: tests/dir4.cwl
   id: directory_secondaryfiles
   doc: Test directories in secondaryFiles
-  tags: [ shell_command, command_line_tool ]
+  tags: [ required, command_line_tool ]
 
 - job: tests/dir-job.yml
   output: {
@@ -1175,7 +1175,7 @@
   tool: tests/dir5.cwl
   id: dynamic_initial_workdir
   doc: Test dynamic initial work dir
-  tags: [ shell_command, initial_work_dir, command_line_tool ]
+  tags: [ initial_work_dir, command_line_tool ]
 
 - job: tests/stagefile-job.yml
   output: {
@@ -1257,14 +1257,14 @@
   tool: tests/envvar.cwl
   id: env_home_tmpdir
   doc: Test $HOME and $TMPDIR are set correctly
-  tags: [ shell_command, command_line_tool ]
+  tags: [ required, command_line_tool ]
 
 - job: tests/empty.json
   output: {}
   tool: tests/envvar2.cwl
   id: env_home_tmpdir_docker
   doc: Test $HOME and $TMPDIR are set correctly in Docker
-  tags: [ shell_command, command_line_tool ]
+  tags: [ required, command_line_tool ]
 
 - job: tests/empty.json
   output:
@@ -1316,14 +1316,14 @@
   tool: tests/docker-array-secondaryfiles.cwl
   id: filesarray_secondaryfiles
   doc: Test required, optional and null secondaryFiles on array of files.
-  tags: [ docker, inline_javascript, shell_command, command_line_tool ]
+  tags: [ docker, inline_javascript, command_line_tool ]
 
 - job: tests/docker-array-secondaryfiles-job2.json
   should_fail: true
   tool: tests/docker-array-secondaryfiles.cwl
   id: filesarray_secondaryfiles2
   doc: Test required, optional and null secondaryFiles on array of files.
-  tags: [ docker, inline_javascript, shell_command, command_line_tool ]
+  tags: [ docker, inline_javascript, command_line_tool ]
 
 - job: tests/dir7.yml
   output: {
@@ -1477,7 +1477,7 @@
   tool: tests/recursive-input-directory.cwl
   id: input_dir_recurs_copy_writable
   doc: Test if a writable input directory is recursively copied and writable
-  tags: [ initial_work_dir, shell_command, command_line_tool ]
+  tags: [ initial_work_dir, command_line_tool ]
 
 - output:
     out: "t\n"
@@ -1819,7 +1819,7 @@
   tool: tests/envvar3.cwl
   id: env_home_tmpdir_docker_no_return_code
   doc: Test $HOME and $TMPDIR are set correctly in Docker without using return code
-  tags: [ shell_command, command_line_tool ]
+  tags: [ required, command_line_tool ]
 
 - job: tests/scatter-valuefrom-job1.json
   output:
@@ -1877,7 +1877,7 @@
   tool: tests/dir4.cwl
   id: job_input_secondary_subdirs
   doc: Test specifying secondaryFiles in subdirectories of the job input document.
-  tags: [ shell_command, command_line_tool ]
+  tags: [ required, command_line_tool ]
 
 - job: tests/dir4-subdir-2-job.yml
   output: {
@@ -1891,7 +1891,7 @@
   tool: tests/dir4.cwl
   id: job_input_subdir_primary_and_secondary_subdirs
   doc: Test specifying secondaryFiles in same subdirectory of the job input as the primary input file.
-  tags: [ shell_command, command_line_tool ]
+  tags: [ required, command_line_tool ]
 
 - job: tests/count-lines3-job.json
   output:
@@ -2773,7 +2773,7 @@
         "location": "lsout",
         "size": 32
       }
-  tags: [ resource, command_line_tool, initial_work_dir ]
+  tags: [ command_line_tool, initial_work_dir ]
   id: initial_work_dir_for_null_and_arrays
 
 - job: tests/stage-array-dirs-job.yml
@@ -2869,7 +2869,7 @@
       "baesname": "symlink.txt"
       "checksum": "sha1$cd28ec34f3f9425aca544b6332453708e8aaa82a"
   should_fail: true
-  tags: [ command_line_tool ]
+  tags: [ required, command_line_tool ]
   id: illegal_symlink
 
 - job: tests/empty.json
@@ -2881,7 +2881,7 @@
       "size": 27
       "basename": "symlink.txt"
       "checksum": "sha1$cd28ec34f3f9425aca544b6332453708e8aaa82a"
-  tags: [ command_line_tool ]
+  tags: [ required, command_line_tool ]
   id: legal_symlink
 
 - job: tests/empty.json
@@ -3399,7 +3399,7 @@
   }
   tool: tests/stdout_chained_commands.cwl
   doc: |
-    Test that chaining two echo calls causes the workflow tool to emit the output to stdout.
+    Test that chaining two echo calls causes the tool to emit the output to stdout.
     This is to confirm that the workflow tool will **not** create an expression such as
     `echo a && echo b > out.txt`, but instead will produce the correct `echo a && echo b`,
     and capture the output correctly.
@@ -3618,4 +3618,28 @@
       an_array_of_trues: [ true, true, true ]
       an_int: 42
 
+- id: cwl_output_json_new_output
+  tool: tests/test-cwl-out5.cwl
+  job: tests/empty.json
+  doc: >-
+    Confirm that undeclared outputs from cwl.output.json are discarded
+  tags: [ required, command_line_tool ]
+  output: {}
+
+- id: cwl_output_json_wrong_type
+  tool: tests/test-cwl-out6.cwl
+  job: tests/empty.json
+  doc: Confirm that outputs from cwl.output.json are type-checked
+  tags: [ required, command_line_tool ]
+  should_fail: true
+
+- id: cwl_output_json_missing_required_output
+  tool: tests/test-cwl-out7.cwl
+  job: tests/empty.json
+  doc: >-
+    Confirm that non-optional outputs not present in cwl.output.json
+    are still checked
+  tags: [ required, command_line_tool ]
+  should_fail: true
+
 - $import: tests/loop/test-index.yaml
diff --git a/invocation.md b/invocation.md
index 8f7e8d7..97a7596 100644
--- a/invocation.md
+++ b/invocation.md
@@ -159,7 +159,9 @@ The exit code of the process is available to expressions in
 If the output directory contains a file named "cwl.output.json", that
 file must be loaded and used as the output object.  In this case, the
 output object should still be type-checked against the `outputs`
-section, but `outputBinding` is ignored.
+section, but `outputBinding` is ignored. Any output is present in the
+"cwl.output.json" file but not declared in the `outputs` section must
+be discarded from the output object.
 
 For Files and Directories, if the value of `path` is a relative path
 pattern (does not begin with a slash '/') then it is resolved relative
diff --git a/tests/dir.cwl b/tests/dir.cwl
index 49ee5dd..3e316b0 100644
--- a/tests/dir.cwl
+++ b/tests/dir.cwl
@@ -1,7 +1,5 @@
 class: CommandLineTool
 cwlVersion: v1.3.0-dev1
-requirements:
-  - class: ShellCommandRequirement
 inputs:
   indir: Directory
 outputs:
@@ -9,9 +7,9 @@ outputs:
     type: File
     outputBinding:
       glob: output.txt
-arguments: ["cd", "$(inputs.indir.path)",
-  {shellQuote: false, valueFrom: "&&"},
-  "find", ".",
-  {shellQuote: false, valueFrom: "|"},
-  "sort"]
-stdout: output.txt
\ No newline at end of file
+arguments:
+  - sh
+  - -c
+  - |
+    cd $(inputs.indir.path) && find . | sort
+stdout: output.txt
diff --git a/tests/dir2.cwl b/tests/dir2.cwl
index 1bd3543..1a95d8b 100644
--- a/tests/dir2.cwl
+++ b/tests/dir2.cwl
@@ -1,7 +1,5 @@
 class: CommandLineTool
 cwlVersion: v1.3.0-dev1
-requirements:
-  ShellCommandRequirement: {}
 hints:
   DockerRequirement:
     dockerPull: docker.io/debian:stable-slim
@@ -12,9 +10,9 @@ outputs:
     type: File
     outputBinding:
       glob: output.txt
-arguments: ["cd", "$(inputs.indir.path)",
-  {shellQuote: false, valueFrom: "&&"},
-  "find", ".",
-  {shellQuote: false, valueFrom: "|"},
-  "sort"]
+arguments:
+  - sh
+  - -c
+  - |
+    cd $(inputs.indir.path) && find . | sort
 stdout: output.txt
diff --git a/tests/dir4.cwl b/tests/dir4.cwl
index 2097996..5743a0d 100644
--- a/tests/dir4.cwl
+++ b/tests/dir4.cwl
@@ -1,7 +1,5 @@
 class: CommandLineTool
 cwlVersion: v1.3.0-dev1
-requirements:
-  - class: ShellCommandRequirement
 inputs:
   inf: File
 outputs:
@@ -9,9 +7,9 @@ outputs:
     type: File
     outputBinding:
       glob: output.txt
-arguments: ["cd", "$(inputs.inf.dirname)/xtestdir",
-  {shellQuote: false, valueFrom: "&&"},
-  "find", ".",
-  {shellQuote: false, valueFrom: "|"},
-  "sort"]
+arguments:
+  - sh
+  - -c
+  - |
+    cd $(inputs.inf.dirname)/xtestdir && find . | sort
 stdout: output.txt
diff --git a/tests/dir5.cwl b/tests/dir5.cwl
index 5b42463..b591c96 100644
--- a/tests/dir5.cwl
+++ b/tests/dir5.cwl
@@ -1,7 +1,6 @@
 class: CommandLineTool
 cwlVersion: v1.3.0-dev1
 requirements:
-  - class: ShellCommandRequirement
   - class: InitialWorkDirRequirement
     listing: $(inputs.indir.listing)
 inputs:
@@ -13,7 +12,9 @@ outputs:
     type: File
     outputBinding:
       glob: output.txt
-arguments: ["find", "-L", ".", "!", "-path", "*.txt",
-  {shellQuote: false, valueFrom: "|"},
-  "sort"]
+arguments:
+  - sh
+  - -c
+  - |
+    find -L . ! -path "*.txt" | sort
 stdout: output.txt
diff --git a/tests/dir6.cwl b/tests/dir6.cwl
index 19d445c..13dcb57 100644
--- a/tests/dir6.cwl
+++ b/tests/dir6.cwl
@@ -18,4 +18,4 @@ arguments: [
   "find", ".",
   {shellQuote: false, valueFrom: "|"},
   "sort"]
-stdout: output.txt
\ No newline at end of file
+stdout: output.txt
diff --git a/tests/docker-array-secondaryfiles.cwl b/tests/docker-array-secondaryfiles.cwl
index fd567a2..b28731d 100644
--- a/tests/docker-array-secondaryfiles.cwl
+++ b/tests/docker-array-secondaryfiles.cwl
@@ -6,7 +6,6 @@ requirements:
   - class: DockerRequirement
     dockerPull: docker.io/debian:stable-slim
   - class: InlineJavascriptRequirement
-  - class: ShellCommandRequirement
 
 class: CommandLineTool
 
@@ -37,14 +36,15 @@ outputs:
       - pattern: "${ return null }"
 
 arguments:
-  - valueFrom: ${
+  - sh
+  - -c
+  - |
+    ${
         var fai_list = "";
         for (var i = 0; i < inputs.fasta_path.length; i ++) {
           fai_list += " cat " + inputs.fasta_path[i].path +".fai" + " >> fai.list && "
         }
         return fai_list.slice(0,-3)
-        }
-    position: 1
-    shellQuote: false
+     }
 
 baseCommand: []
diff --git a/tests/envvar.cwl b/tests/envvar.cwl
index e4785b7..0cf14f9 100644
--- a/tests/envvar.cwl
+++ b/tests/envvar.cwl
@@ -2,10 +2,8 @@ class: CommandLineTool
 cwlVersion: v1.3.0-dev1
 inputs: []
 outputs: []
-requirements:
-  ShellCommandRequirement: {}
-arguments: [
-  echo, {valueFrom: '"HOME=$HOME"', shellQuote: false}, {valueFrom: '"TMPDIR=$TMPDIR"', shellQuote: false},
-  {valueFrom: '&&', shellQuote: false},
-  test, {valueFrom: '"$HOME"', shellQuote: false}, "=", $(runtime.outdir),
-  "-a", {valueFrom: '"$TMPDIR"', shellQuote: false}, "=", $(runtime.tmpdir)]
+arguments:
+  - sh
+  - -c
+  - |
+    echo "HOME=$HOME" "TMPDIR=$TMPDIR" && test "$HOME"=$(runtime.outdir) -a "$TMPDIR"=$(runtime.tmpdir)
diff --git a/tests/envvar2.cwl b/tests/envvar2.cwl
index f06f5c0..8b81c79 100644
--- a/tests/envvar2.cwl
+++ b/tests/envvar2.cwl
@@ -2,13 +2,11 @@ class: CommandLineTool
 cwlVersion: v1.3.0-dev1
 inputs: []
 outputs: []
-requirements:
-  ShellCommandRequirement: {}
 hints:
   DockerRequirement:
     dockerPull: docker.io/debian:stable-slim
-arguments: [
-  echo, {valueFrom: '"HOME=$HOME"', shellQuote: false}, {valueFrom: '"TMPDIR=$TMPDIR"', shellQuote: false},
-  {valueFrom: '&&', shellQuote: false},
-  test, {valueFrom: '"$HOME"', shellQuote: false}, "=", $(runtime.outdir),
-  "-a", {valueFrom: '"$TMPDIR"', shellQuote: false}, "=", $(runtime.tmpdir)]
+arguments:
+  - sh
+  - -c
+  - |
+    echo "HOME=$HOME" "TMPDIR=$TMPDIR" && test "$HOME"=$(runtime.outdir) -a "$TMPDIR"=$(runtime.tmpdir)
diff --git a/tests/envvar3.cwl b/tests/envvar3.cwl
index 5863f34..926246a 100644
--- a/tests/envvar3.cwl
+++ b/tests/envvar3.cwl
@@ -6,18 +6,17 @@ outputs:
   results:
     type: File
     outputBinding: { glob: results }
-requirements:
-  ShellCommandRequirement: {}
 hints:
   DockerRequirement:
     dockerPull: docker.io/debian:stable-slim
 arguments:
-  - shellQuote: false
-    valueFrom: |
-      echo HOME=$HOME TMPDIR=$TMPDIR > log
-      if [ "$HOME" = "$(runtime.outdir)" ] && [ "$TMPDIR" = "$(runtime.tmpdir)" ]
-      then
-          echo success > results
-      else
-          echo failure > results
-      fi
+  - sh
+  - -c
+  - |
+    echo HOME=$HOME TMPDIR=$TMPDIR > log ;
+    if [ "$HOME" = "$(runtime.outdir)" ] && [ "$TMPDIR" = "$(runtime.tmpdir)" ] ;
+    then
+        echo success > results ;
+    else
+        echo failure > results ;
+    fi ;
diff --git a/tests/exitcode.cwl b/tests/exitcode.cwl
index bf4563b..981ad39 100644
--- a/tests/exitcode.cwl
+++ b/tests/exitcode.cwl
@@ -1,7 +1,5 @@
 cwlVersion: v1.3.0-dev1
 class: CommandLineTool
-requirements:
-  ShellCommandRequirement: {}
 inputs: []
 outputs:
   code:
@@ -9,4 +7,8 @@ outputs:
     outputBinding:
       outputEval: $(runtime.exitCode)
 successCodes: [7]
-arguments: ["exit", "7"]
+arguments:
+  - sh
+  - -c
+  - |
+    exit 7
diff --git a/tests/initialwork-path.cwl b/tests/initialwork-path.cwl
index 0f3113b..54ce894 100644
--- a/tests/initialwork-path.cwl
+++ b/tests/initialwork-path.cwl
@@ -5,11 +5,11 @@ requirements:
     listing:
       - entry: $(inputs.file1)
         entryname: bob.txt
-  ShellCommandRequirement: {}
 inputs:
   file1: File
 outputs: []
 arguments:
-  - shellQuote: false
-    valueFrom: |
-      test "$(inputs.file1.path)" = "$(runtime.outdir)/bob.txt"
+  - sh
+  - -c
+  - |
+    test "$(inputs.file1.path)" = "$(runtime.outdir)/bob.txt"
diff --git a/tests/iwd/iwd-container-entryname1.cwl b/tests/iwd/iwd-container-entryname1.cwl
index a012d91..d2215e6 100644
--- a/tests/iwd/iwd-container-entryname1.cwl
+++ b/tests/iwd/iwd-container-entryname1.cwl
@@ -18,6 +18,8 @@ requirements:
     listing:
       - entryname: /tmp2j3y7rpb/input/stuff.txt  # Give it a weird prefix to minimize chance of conflict with a real file
         entry: $(inputs.filelist)
-  ShellCommandRequirement: {}
 arguments:
-  - {shellQuote: false, valueFrom: "head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt"}
+  - sh
+  - -c
+  - |
+    head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt
diff --git a/tests/iwd/iwd-container-entryname2.cwl b/tests/iwd/iwd-container-entryname2.cwl
index dbbc716..db5f6e2 100644
--- a/tests/iwd/iwd-container-entryname2.cwl
+++ b/tests/iwd/iwd-container-entryname2.cwl
@@ -15,6 +15,8 @@ requirements:
     listing:
       - entryname: /tmp2j3y7rpb/input/stuff.txt  # Give it a weird prefix to minimize chance of conflict with a real file
         entry: $(inputs.filelist)
-  ShellCommandRequirement: {}
 arguments:
-  - {shellQuote: false, valueFrom: "head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt"}
+  - sh
+  - -c
+  - |
+    head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt
diff --git a/tests/iwd/iwd-container-entryname3.cwl b/tests/iwd/iwd-container-entryname3.cwl
index 5001fed..2e03170 100644
--- a/tests/iwd/iwd-container-entryname3.cwl
+++ b/tests/iwd/iwd-container-entryname3.cwl
@@ -19,6 +19,8 @@ requirements:
     listing:
       - entryname: /tmp2j3y7rpb/input/stuff.txt  # Give it a weird prefix to minimize chance of conflict with a real file
         entry: $(inputs.filelist)
-  ShellCommandRequirement: {}
 arguments:
-  - {shellQuote: false, valueFrom: "head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt"}
+  - sh
+  - -c
+  - |
+    head -n10 /tmp2j3y7rpb/input/stuff.txt > /output/head.txt
diff --git a/tests/iwd/iwd-container-entryname4.cwl b/tests/iwd/iwd-container-entryname4.cwl
index f35c048..5e32c4d 100644
--- a/tests/iwd/iwd-container-entryname4.cwl
+++ b/tests/iwd/iwd-container-entryname4.cwl
@@ -14,6 +14,8 @@ requirements:
     listing:
       - entryname: ../input/stuff.txt  # Illegal
         entry: $(inputs.filelist)
-  ShellCommandRequirement: {}
 arguments:
-  - {shellQuote: false, valueFrom: "head -n10 ../input/stuff.txt > head.txt"}
+  - sh
+  - -c
+  - |
+    head -n10 ../input/stuff.txt > head.txt
diff --git a/tests/iwd/test-index.yaml b/tests/iwd/test-index.yaml
index 68eface..116a5c8 100644
--- a/tests/iwd/test-index.yaml
+++ b/tests/iwd/test-index.yaml
@@ -391,4 +391,4 @@
       }
     ]
   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 ]
diff --git a/tests/recursive-input-directory.cwl b/tests/recursive-input-directory.cwl
index 3d89f38..9cd30da 100644
--- a/tests/recursive-input-directory.cwl
+++ b/tests/recursive-input-directory.cwl
@@ -6,22 +6,22 @@ requirements:
       - entry: $(inputs.input_dir)
         entryname: work_dir
         writable: true
-  ShellCommandRequirement: {}
 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;
+ - sh
+ - -c
+ - |
+   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:
diff --git a/tests/runtime-paths-distinct.cwl b/tests/runtime-paths-distinct.cwl
index 215df76..1c775c8 100644
--- a/tests/runtime-paths-distinct.cwl
+++ b/tests/runtime-paths-distinct.cwl
@@ -1,13 +1,12 @@
 class: CommandLineTool
 cwlVersion: v1.3.0-dev1
-requirements:
-  ShellCommandRequirement: {}
 inputs: {}
 outputs:
   foo: File
 arguments:
-  - shellQuote: false
-    valueFrom: |
-      echo "cow" > "$(runtime.outdir)/foo" &&
-      echo "moo" > "$(runtime.tmpdir)/foo" &&
-      echo '{"foo": {"path": "$(runtime.outdir)/foo", "class": "File"} }' > cwl.output.json
+  - sh
+  - -c
+  - |
+    echo "cow" > "$(runtime.outdir)/foo" &&
+    echo "moo" > "$(runtime.tmpdir)/foo" &&
+    echo '{"foo": {"path": "$(runtime.outdir)/foo", "class": "File"} }' > cwl.output.json
diff --git a/tests/secondaryfiles/rename-inputs.cwl b/tests/secondaryfiles/rename-inputs.cwl
index f45afe8..703c450 100644
--- a/tests/secondaryfiles/rename-inputs.cwl
+++ b/tests/secondaryfiles/rename-inputs.cwl
@@ -43,12 +43,10 @@ inputs:
 
 
 arguments:
-- "ls"
-- $(inputs.inputWithSecondary.dirname)
-- valueFrom: "|"
-  shellQuote: false
-- "grep"
-- "secondary"
+ - sh
+ - -c
+ - |
+   ls $(inputs.inputWithSecondary.dirname) | grep secondary
 
 outputs:
 - id: output_file
@@ -56,4 +54,3 @@ outputs:
 stdout: result
 requirements:
   InlineJavascriptRequirement: {}
-  ShellCommandRequirement: {}
diff --git a/tests/secondaryfiles/test-index.yaml b/tests/secondaryfiles/test-index.yaml
index 54fb40e..8dd220c 100644
--- a/tests/secondaryfiles/test-index.yaml
+++ b/tests/secondaryfiles/test-index.yaml
@@ -8,7 +8,7 @@
       checksum: sha1$901c3d387a263c57eaed6f24a82517c1fb0e198d
       size: 54
       location: result
-  tags: [ inline_javascript, secondary_files, command_line_tool, shell_command ]
+  tags: [ inline_javascript, secondary_files, command_line_tool ]
 
 - tool: rename-outputs.cwl
   doc: Confirm CommandOutputParameter expression can receive a File object
diff --git a/tests/stage-array.cwl b/tests/stage-array.cwl
index 745a34b..1c19ce4 100644
--- a/tests/stage-array.cwl
+++ b/tests/stage-array.cwl
@@ -4,7 +4,10 @@ class: CommandLineTool
 cwlVersion: v1.3.0-dev1
 id: stage_array
 arguments:
-  - {shellQuote: false, valueFrom: "ls | grep -v lsout"}
+  - sh
+  - -c
+  - |
+    ls | grep -v lsout
 inputs:
   - id: input_file
     type: File
@@ -30,4 +33,3 @@ requirements:
       - entry: $(null)
       - entryname: a
         entry: b
-  - class: ShellCommandRequirement
diff --git a/tests/stderr-mediumcut.cwl b/tests/stderr-mediumcut.cwl
index cd0421e..97af38c 100644
--- a/tests/stderr-mediumcut.cwl
+++ b/tests/stderr-mediumcut.cwl
@@ -1,13 +1,14 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.3.0-dev1
-doc: "Test of capturing stderr output in a docker container."
-requirements:
-  ShellCommandRequirement: {}
+doc: "Test of capturing stderr output"
 inputs: []
 outputs:
   output_file:
     type: stderr
 arguments:
- - { valueFrom: "echo foo 1>&2", shellQuote: False }
+ - sh
+ - -c
+ - |
+   echo foo 1>&2
 stderr: std.err
diff --git a/tests/stderr-shortcut.cwl b/tests/stderr-shortcut.cwl
index d768331..a09684b 100644
--- a/tests/stderr-shortcut.cwl
+++ b/tests/stderr-shortcut.cwl
@@ -2,11 +2,12 @@
 class: CommandLineTool
 cwlVersion: v1.3.0-dev1
 doc: "Test of capturing stderr output."
-requirements:
-  ShellCommandRequirement: {}
 inputs: []
 outputs:
   output_file:
     type: stderr
 arguments:
- - { valueFrom: "echo foo 1>&2", shellQuote: False }
+ - sh
+ - -c
+ - |
+   echo foo 1>&2
diff --git a/tests/stderr.cwl b/tests/stderr.cwl
index 4d7546d..d2a82ea 100644
--- a/tests/stderr.cwl
+++ b/tests/stderr.cwl
@@ -2,13 +2,14 @@
 class: CommandLineTool
 cwlVersion: v1.3.0-dev1
 doc: "Test of capturing stderr output."
-requirements:
-  ShellCommandRequirement: {}
 inputs: []
 outputs:
   output_file:
     type: File
     outputBinding: {glob: error.txt}
 arguments:
- - { valueFrom: "echo foo 1>&2", shellQuote: False }
+ - sh
+ - -c
+ - |
+   echo foo 1>&2
 stderr: error.txt
diff --git a/tests/symlink-illegal.cwl b/tests/symlink-illegal.cwl
index e02cea5..ec2737b 100644
--- a/tests/symlink-illegal.cwl
+++ b/tests/symlink-illegal.cwl
@@ -11,15 +11,8 @@ outputs:
     type: File
     outputBinding: {glob: symlink.txt}
 
-requirements:
-  - class: ShellCommandRequirement
-
 arguments:
-  - echo
-  - "Who's gonna drive you home"
-  - {valueFrom: "> /tmp/original.txt", shellQuote: false}
-  - {valueFrom: " && ", shellQuote: false}
-  - ln
-  - -s
-  - /tmp/original.txt
-  - symlink.txt
+  - sh
+  - -c
+  - |
+    echo "Who's gonna drive you home" > /tmp/original.txt && ln -s /tmp/original.txt symlink.txt
diff --git a/tests/symlink-legal.cwl b/tests/symlink-legal.cwl
index eceacfb..aa25cf3 100644
--- a/tests/symlink-legal.cwl
+++ b/tests/symlink-legal.cwl
@@ -11,18 +11,8 @@ outputs:
     type: File
     outputBinding: {glob: symlink.txt}
 
-requirements:
-  - class: ShellCommandRequirement
-
 arguments:
-  - mkdir
-  - adir
-  - {valueFrom: " && ", shellQuote: false}
-  - echo
-  - "Who's gonna drive you home"
-  - {valueFrom: "> adir/original.txt", shellQuote: false}
-  - {valueFrom: " && ", shellQuote: false}
-  - ln
-  - -s
-  - adir/original.txt
-  - symlink.txt
+  - sh
+  - -c
+  - |
+    mkdir adir && echo "Who's gonna drive you home" > adir/original.txt && ln -s adir/original.txt symlink.txt
diff --git a/tests/test-cwl-out.cwl b/tests/test-cwl-out.cwl
index 0ee3bb2..ace607e 100644
--- a/tests/test-cwl-out.cwl
+++ b/tests/test-cwl-out.cwl
@@ -1,7 +1,5 @@
 class: CommandLineTool
 cwlVersion: v1.3.0-dev1
-requirements:
-  - class: ShellCommandRequirement
 hints:
   DockerRequirement:
     dockerPull: docker.io/debian:stable-slim
@@ -13,6 +11,7 @@ outputs:
     type: File
 
 arguments:
-   - valueFrom: >
-       echo foo > foo && echo '{"foo": {"path": "$(runtime.outdir)/foo", "class": "File"} }' > cwl.output.json
-     shellQuote: false
+   - sh
+   - -c
+   - |
+     echo foo > foo && echo '{"foo": {"path": "$(runtime.outdir)/foo", "class": "File"} }' > cwl.output.json
diff --git a/tests/test-cwl-out2.cwl b/tests/test-cwl-out2.cwl
index 71b6d71..e518866 100644
--- a/tests/test-cwl-out2.cwl
+++ b/tests/test-cwl-out2.cwl
@@ -1,7 +1,5 @@
 class: CommandLineTool
 cwlVersion: v1.3.0-dev1
-requirements:
-  - class: ShellCommandRequirement
 hints:
   DockerRequirement:
     dockerPull: docker.io/debian:stable-slim
@@ -13,6 +11,7 @@ outputs:
     type: File
 
 arguments:
-   - valueFrom: >
-       echo foo > foo && echo '{"foo": {"location": "file://$(runtime.outdir)/foo", "class": "File"} }' > cwl.output.json
-     shellQuote: false
+   - sh
+   - -c
+   - |
+     echo foo > foo && echo '{"foo": {"location": "file://$(runtime.outdir)/foo", "class": "File"} }' > cwl.output.json
diff --git a/tests/test-cwl-out3.cwl b/tests/test-cwl-out3.cwl
index 4ff5ea1..0ae1979 100644
--- a/tests/test-cwl-out3.cwl
+++ b/tests/test-cwl-out3.cwl
@@ -1,7 +1,5 @@
 class: CommandLineTool
 cwlVersion: v1.3.0-dev1
-requirements:
-  - class: ShellCommandRequirement
 hints:
   DockerRequirement:
     dockerPull: docker.io/debian:stable-slim
diff --git a/tests/test-cwl-out4.cwl b/tests/test-cwl-out4.cwl
index 756baaa..658d508 100644
--- a/tests/test-cwl-out4.cwl
+++ b/tests/test-cwl-out4.cwl
@@ -1,7 +1,5 @@
 class: CommandLineTool
 cwlVersion: v1.3.0-dev1
-requirements:
-  - class: ShellCommandRequirement
 hints:
   DockerRequirement:
     dockerPull: docker.io/debian:stable-slim
diff --git a/tests/test-cwl-out5.cwl b/tests/test-cwl-out5.cwl
new file mode 100644
index 0000000..aee2d06
--- /dev/null
+++ b/tests/test-cwl-out5.cwl
@@ -0,0 +1,18 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+hints:
+  DockerRequirement:
+    dockerPull: docker.io/debian:stable-slim
+
+inputs: []
+
+baseCommand: sh
+
+arguments:
+   - -c
+   - |
+     echo foo > foo && echo '{"foo": {"location": "foo", "class": "File"} }'
+
+stdout: cwl.output.json
+
+outputs: {}
diff --git a/tests/test-cwl-out6.cwl b/tests/test-cwl-out6.cwl
new file mode 100644
index 0000000..17fedbd
--- /dev/null
+++ b/tests/test-cwl-out6.cwl
@@ -0,0 +1,20 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+hints:
+  DockerRequirement:
+    dockerPull: docker.io/debian:stable-slim
+
+inputs: []
+
+baseCommand: sh
+
+arguments:
+   - -c
+   - |
+     echo foo > foo && echo '{"foo": {"location": "foo", "class": "File"} }'
+
+stdout: cwl.output.json
+
+outputs:
+  - id: foo
+    type: int
diff --git a/tests/test-cwl-out7.cwl b/tests/test-cwl-out7.cwl
new file mode 100644
index 0000000..d45a9ae
--- /dev/null
+++ b/tests/test-cwl-out7.cwl
@@ -0,0 +1,22 @@
+class: CommandLineTool
+cwlVersion: v1.3.0-dev1
+hints:
+  DockerRequirement:
+    dockerPull: docker.io/debian:stable-slim
+
+inputs: []
+
+baseCommand: sh
+
+arguments:
+   - -c
+   - |
+     echo foo > foo && echo '{"foo": {"location": "foo", "class": "File"} }'
+
+stdout: cwl.output.json
+
+outputs:
+  - id: foo
+    type: File
+  - id: bar
+    type: int