use CWL version 1.2 everywhere

mr-c · mr-c · commit c46b733d36ae · 2022-11-22T19:21:06.000+01:00
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -148,8 +148,11 @@ are still working after the change.
 Use “tool description” not “tool wrapper” for describing the first argument
 given to the `cwl-runner` or `cwltool` commands.
 
+
 ### Code Examples
 
+All CWL documents should be version 1.2 unless there is a very good reason otherwise.
+
 To include code into a Markdown file you have two options. For external files use
 the following command:
 
diff --git a/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl b/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 label: Example trivial wrapper for Java 9 compiler
 hints:
diff --git a/src/_includes/cwl/creating-files-at-runtime/createfile.cwl b/src/_includes/cwl/creating-files-at-runtime/createfile.cwl
@@ -1,5 +1,6 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
 class: CommandLineTool
-cwlVersion: v1.0
 baseCommand: ["sh", "example.sh"]
 
 requirements:
diff --git a/src/_includes/cwl/custom-types/custom-types.cwl b/src/_includes/cwl/custom-types/custom-types.cwl
@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 
 requirements:
diff --git a/src/_includes/cwl/environment-variables/env.cwl b/src/_includes/cwl/environment-variables/env.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 baseCommand: env
 requirements:
diff --git a/src/_includes/cwl/expressions/expression.cwl b/src/_includes/cwl/expressions/expression.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 baseCommand: echo
 
diff --git a/src/_includes/cwl/file-formats/metadata_example.cwl b/src/_includes/cwl/file-formats/metadata_example.cwl
@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 
 label: An example tool demonstrating metadata.
diff --git a/src/_includes/cwl/inputs/array-inputs.cwl b/src/_includes/cwl/inputs/array-inputs.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 inputs:
   filesA:
diff --git a/src/_includes/cwl/inputs/inp.cwl b/src/_includes/cwl/inputs/inp.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 baseCommand: echo
 inputs:
diff --git a/src/_includes/cwl/inputs/record.cwl b/src/_includes/cwl/inputs/record.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 inputs:
   dependent_parameters:
diff --git a/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl b/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl
@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 
 label: An example tool demonstrating metadata.
diff --git a/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl b/src/_includes/cwl/metadata-and-authorship/metadata_example3.cwl
@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 
 label: An example tool demonstrating metadata.
diff --git a/src/_includes/cwl/outputs/array-outputs.cwl b/src/_includes/cwl/outputs/array-outputs.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 baseCommand: touch
 inputs:
diff --git a/src/_includes/cwl/outputs/stdout.cwl b/src/_includes/cwl/outputs/stdout.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 baseCommand: echo
 stdout: output.txt
diff --git a/src/_includes/cwl/outputs/tar.cwl b/src/_includes/cwl/outputs/tar.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 baseCommand: [tar, --extract]
 inputs:
diff --git a/src/_includes/cwl/parameter-references/tar-param.cwl b/src/_includes/cwl/parameter-references/tar-param.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 baseCommand: [tar, --extract]
 inputs:
diff --git a/src/_includes/cwl/specifying-software-requirements/custom-types.cwl b/src/_includes/cwl/specifying-software-requirements/custom-types.cwl
@@ -1,4 +1,5 @@
-cwlVersion: v1.0
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
 class: CommandLineTool
 
 label: "InterProScan: protein sequence classifier"
diff --git a/src/_includes/cwl/staging-input-files/linkfile.cwl b/src/_includes/cwl/staging-input-files/linkfile.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 hints:
   DockerRequirement:
diff --git a/src/_includes/cwl/using-containers/docker.cwl b/src/_includes/cwl/using-containers/docker.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 baseCommand: node
 hints:
diff --git a/src/_includes/cwl/workflows/1st-workflow.cwl b/src/_includes/cwl/workflows/1st-workflow.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 inputs:
   tarball: File
diff --git a/src/_includes/cwl/workflows/arguments.cwl b/src/_includes/cwl/workflows/arguments.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 label: Example trivial wrapper for Java 9 compiler
 hints:
diff --git a/src/_includes/cwl/workflows/hello_world.cwl b/src/_includes/cwl/workflows/hello_world.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 baseCommand: echo
 inputs:
diff --git a/src/_includes/cwl/workflows/hello_world_to_stdout.cwl b/src/_includes/cwl/workflows/hello_world_to_stdout.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 baseCommand: echo
 inputs:
diff --git a/src/_includes/cwl/workflows/nestedworkflows.cwl b/src/_includes/cwl/workflows/nestedworkflows.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 
 inputs: []
diff --git a/src/_includes/cwl/workflows/scatter-nested-workflow.cwl b/src/_includes/cwl/workflows/scatter-nested-workflow.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 
 requirements:
diff --git a/src/_includes/cwl/workflows/scatter-two-steps.cwl b/src/_includes/cwl/workflows/scatter-two-steps.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 
 requirements:
diff --git a/src/_includes/cwl/workflows/scatter-workflow.cwl b/src/_includes/cwl/workflows/scatter-workflow.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: Workflow
 
 requirements:
diff --git a/src/_includes/cwl/workflows/tar-param.cwl b/src/_includes/cwl/workflows/tar-param.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 baseCommand: [tar, --extract]
 inputs:
diff --git a/src/_includes/cwl/workflows/wc-tool.cwl b/src/_includes/cwl/workflows/wc-tool.cwl
@@ -1,6 +1,5 @@
 #!/usr/bin/env cwl-runner
-
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 baseCommand: wc
 arguments: ["-c"]
