Merge pull request #47 from common-workflow-language/stable-release

Approve CWL v1.2 stable release
common-workflow-language · Aug 7, 2020 · bfe4075 · bfe4075
2 parents 729bb8d + 317dce2
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diff --git a/CommandLineTool.yml b/CommandLineTool.yml
@@ -10,10 +10,10 @@ $graph:
   type: documentation
   doc:
     - |
-      # Common Workflow Language (CWL) Command Line Tool Description, v1.2.0-dev5
+      # Common Workflow Language (CWL) Command Line Tool Description, v1.2
 
       This version:
-        * https://w3id.org/cwl/v1.2.0-dev5/
+        * https://w3id.org/cwl/v1.2/
 
       Latest stable version:
         * https://w3id.org/cwl/
@@ -37,17 +37,17 @@ $graph:
     - {$include: intro.md}
 
     - |
-      ## Introduction to the CWL Command Line Tool standard v1.2.0-dev5
+      ## Introduction to the CWL Command Line Tool standard v1.2
 
       This specification represents the latest development release from the
-      CWL group.  Since the v1.1 release, v1.2.0-dev5 introduces the
+      CWL group.  Since the v1.1 release, v1.2 introduces the
       following updates to the CWL Command Line Tool standard.
-      Documents should use `cwlVersion: v1.2.0-dev5` to make use of new
-      syntax and features introduced in v1.2.0-dev5.  Existing v1.1 documents
+      Documents should use `cwlVersion: v1.2` to make use of new
+      syntax and features introduced in v1.2.  Existing v1.1 documents
       should be trivially updatable by changing `cwlVersion`, however
       CWL documents that relied on previously undefined or
       underspecified behavior may have slightly different behavior in
-      v1.2.0-dev5.
+      v1.2.
 
       ## Changelog
 
@@ -81,7 +81,7 @@ $graph:
         running in containers.
       * Specify default success/fail interpretation of exit codes when not given.
 
-      See also the [CWL Workflow Description, v1.2.0-dev5 changelog](Workflow.html#Changelog).
+      See also the [CWL Workflow Description, v1.2 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/Process.yml b/Process.yml
@@ -8,7 +8,7 @@ $namespaces:
 
 $graph:
 
-- name: "Common Workflow Language, v1.2.0-dev5"
+- name: "Common Workflow Language, v1.2"
   type: documentation
   doc: {$include: concepts.md}
 
@@ -45,6 +45,7 @@ $graph:
     - cwl:v1.2.0-dev3
     - cwl:v1.2.0-dev4
     - cwl:v1.2.0-dev5
+    - cwl:v1.2
 
 - name: CWLType
   type: enum

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 Hello!
 
-This repo holds the unreleased v1.2 of the Common Workflow Language standard and the history of its development.
+This repo holds the released v1.2 of the Common Workflow Language standard and the history of its development.
 
 You can render this using https://github.com/common-workflow-language/cwl-website/blob/master/website.sh
 
-You may browse the spec online at https://www.commonwl.org/v1.2.0-dev5
+You may browse the spec online at https://www.commonwl.org/v1.2
diff --git a/Workflow.yml b/Workflow.yml
@@ -11,10 +11,10 @@ $graph:
   type: documentation
   doc:
     - |
-      # Common Workflow Language (CWL) Workflow Description, v1.2.0-dev5
+      # Common Workflow Language (CWL) Workflow Description, v1.2
 
       This version:
-        * https://w3id.org/cwl/v1.2.0-dev5/
+        * https://w3id.org/cwl/v1.2/
 
       Latest stable version:
         * https://w3id.org/cwl/
@@ -35,17 +35,17 @@ $graph:
 
     - |
 
-      ## Introduction to CWL Workflow standard v1.2.0-dev5
+      ## Introduction to CWL Workflow standard v1.2
 
       This specification represents the latest stable release from the
-      CWL group.  Since the v1.1 release, v1.2.0-dev5 introduces the
+      CWL group.  Since the v1.1 release, v1.2 introduces the
       following updates to the CWL Workflow standard.
-      Documents should to use `cwlVersion: v1.2.0-dev5` to make use of new
-      syntax and features introduced in v1.2.0-dev5.  Existing v1.1 documents
+      Documents should to use `cwlVersion: v1.2` to make use of new
+      syntax and features introduced in v1.2.  Existing v1.1 documents
       should be trivially updatable by changing `cwlVersion`, however
       CWL documents that relied on previously undefined or
       underspecified behavior may have slightly different behavior in
-      v1.2.0-dev5.
+      v1.2.
 
       ## Changelog
 
@@ -72,7 +72,7 @@ $graph:
         * Added discussion about handling different document versions.
         * Added definition of **data link**
 
-      See also the [CWL Command Line Tool Description, v1.2.0-dev5 changelog](CommandLineTool.html#Changelog).
+      See also the [CWL Command Line Tool Description, v1.2 changelog](CommandLineTool.html#Changelog).
       For other changes since CWL v1.0, see the
       [CWL Workflow Description, v1.1 changelog](https://www.commonwl.org/v1.1/Workflow.html#Changelog)
 

diff --git a/contrib.md b/contrib.md
@@ -13,17 +13,12 @@ Contributors to v1.2:
 
 Incorporates the work of past authors and contributors to [CWL v1.0](https://www.commonwl.org/v1.0/Workflow.html) and [CWL v1.1](https://www.commonwl.org/v1.1/Workflow.html).
 
-This specification is a draft, and has not yet been approved as an official CWL standard.
-
-<!-- v1.2.0-devN is not yet approvied
-This specification was [approved on 6 June 2019](https://github.com/common-workflow-language/common-workflow-language/issues/861) by the CWL leadership team consisting of:
+This specification was [approved on XXX August 2020](https://github.com/common-workflow-language/cwl-v1.2/XXX) by the CWL leadership team consisting of:
 
 * Peter Amstutz, Curii Inc. / Arvados; https://orcid.org/0000-0003-3566-7705
 * John Chilton, Pennsylvania State University / Galaxy Project; https://orcid.org/0000-0002-6794-0756
 * Michael R. Crusoe, CWL Project Lead; https://orcid.org/0000-0002-2961-9670
 * Brandi Davis Dusenbery, Seven Bridges Genomics, Inc.; https://orcid.org/0000-0001-7811-8613
-* Jeff Gentry, Broad Institute; https://orcid.org/0000-0001-5351-8442
+* Jeff Gentry, Foundation Medicine; https://orcid.org/0000-0001-5351-8442
 * Hervé Ménager, Institut Pasteur; https://orcid.org/0000-0002-7552-1009
 * Stian Soiland-Reyes, University of Manchester; https://orcid.org/0000-0001-9842-9718
-
--->
diff --git a/cwl-runner.cwl b/cwl-runner.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 
 doc: |
  Generic interface to run a Common Workflow Language tool or workflow from the

diff --git a/index.md b/index.md
@@ -1,9 +1,9 @@
-# Common Workflow Language Specifications, v1.2.0-dev5
+# Common Workflow Language Specifications, v1.2
 
 The CWL specifications are divided up into several documents.
 
 The [User Guide](http://www.commonwl.org/user_guide/) provides a gentle
-introduction to writing CWL command line tools and workflows. Currently it is for CWL v1.0 only.
+introduction to writing CWL command line tools and workflows. Currently it covers CWL v1.0 only.
 
 The [Command Line Tool Description Specification](CommandLineTool.html)
 specifies the document schema and execution semantics for wrapping and

diff --git a/tests/anon_enum_inside_array.cwl b/tests/anon_enum_inside_array.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 class: CommandLineTool
 inputs:
   first:

diff --git a/tests/anon_enum_inside_array_inside_schemadef.cwl b/tests/anon_enum_inside_array_inside_schemadef.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 class: CommandLineTool
 requirements:
   SchemaDefRequirement:

diff --git a/tests/any-type-compat.cwl b/tests/any-type-compat.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 class: Workflow
 
 steps: []

diff --git a/tests/basename-fields-job.yml b/tests/basename-fields-job.yml
@@ -1,4 +1,4 @@
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 tool:
   class: File
   path: echo-tool.cwl  # could have been any file, this isn't a secret CWL feature :-)
diff --git a/tests/basename-fields-test.cwl b/tests/basename-fields-test.cwl
@@ -1,4 +1,4 @@
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 class: Workflow
 
 requirements:

diff --git a/tests/binding-test.cwl b/tests/binding-test.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 
 class: CommandLineTool
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 hints:
   - class: DockerRequirement
     dockerPull: python:2-slim

diff --git a/tests/bool-empty-inputbinding.cwl b/tests/bool-empty-inputbinding.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 hints:
   - class: DockerRequirement
     dockerPull: python:2-slim

diff --git a/tests/bwa-mem-tool.cwl b/tests/bwa-mem-tool.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 
 class: CommandLineTool
 

diff --git a/tests/cat-from-dir.cwl b/tests/cat-from-dir.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 
 class: CommandLineTool
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 
 inputs:
   dir1: Directory

diff --git a/tests/cat-tool-shortcut.cwl b/tests/cat-tool-shortcut.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 
 class: CommandLineTool
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 
 requirements:
   - class: DockerRequirement

diff --git a/tests/cat-tool.cwl b/tests/cat-tool.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 
 class: CommandLineTool
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 
 inputs:
   file1: File

diff --git a/tests/cat1-testcli.cwl b/tests/cat1-testcli.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 {
     "class": "CommandLineTool",
-    "cwlVersion": "v1.2.0-dev5",
+    "cwlVersion": "v1.2",
     "doc": "Print the contents of a file to stdout using 'cat' running in a docker container.",
     "hints": [
         {

diff --git a/tests/cat3-from-dir.cwl b/tests/cat3-from-dir.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 inputs:
   dir1:
     type: Directory

diff --git a/tests/cat3-nodocker.cwl b/tests/cat3-nodocker.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 doc: "Print the contents of a file to stdout using 'cat'."
 inputs:
   file1:

diff --git a/tests/cat3-tool-docker.cwl b/tests/cat3-tool-docker.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
 requirements:
   DockerRequirement:

diff --git a/tests/cat3-tool-mediumcut.cwl b/tests/cat3-tool-mediumcut.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
 requirements:
   DockerRequirement:

diff --git a/tests/cat3-tool-shortcut.cwl b/tests/cat3-tool-shortcut.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
 requirements:
   DockerRequirement:

diff --git a/tests/cat3-tool.cwl b/tests/cat3-tool.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   DockerRequirement:

diff --git a/tests/cat4-tool.cwl b/tests/cat4-tool.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 doc: "Print the contents of a file to stdout using 'cat' running in a docker container if docker is available."
 hints:
   DockerRequirement:

diff --git a/tests/cat5-tool.cwl b/tests/cat5-tool.cwl
@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 $namespaces:
   ex: http://example.com/
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 class: CommandLineTool
 doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:

diff --git a/tests/conditionals/action.cwl b/tests/conditionals/action.cwl
@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 inputs:
   initial_file: File
   out_file_name: string

diff --git a/tests/conditionals/bar.cwl b/tests/conditionals/bar.cwl
@@ -1,5 +1,5 @@
 class: CommandLineTool
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 inputs:
   in1: int
 baseCommand: [echo]

diff --git a/tests/conditionals/cat.cwl b/tests/conditionals/cat.cwl
@@ -1,5 +1,5 @@
 class: CommandLineTool
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 inputs:
   in1: int
   in2: int

diff --git a/tests/conditionals/cond-wf-001.cwl b/tests/conditionals/cond-wf-001.cwl
@@ -1,5 +1,5 @@
 class: Workflow
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 inputs:
   val: int
 

diff --git a/tests/conditionals/cond-wf-001_nojs.cwl b/tests/conditionals/cond-wf-001_nojs.cwl
@@ -1,5 +1,5 @@
 class: Workflow
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 inputs:
   test: boolean
 

diff --git a/tests/conditionals/cond-wf-002.cwl b/tests/conditionals/cond-wf-002.cwl
@@ -1,5 +1,5 @@
 class: Workflow
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 inputs:
   val: int
 

diff --git a/tests/conditionals/cond-wf-002_nojs.cwl b/tests/conditionals/cond-wf-002_nojs.cwl
@@ -1,5 +1,5 @@
 class: Workflow
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 inputs:
   val: int
   test:

diff --git a/tests/conditionals/cond-wf-003.1.cwl b/tests/conditionals/cond-wf-003.1.cwl
@@ -1,5 +1,5 @@
 class: Workflow
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 inputs:
   val: int
 

diff --git a/tests/conditionals/cond-wf-003.1_nojs.cwl b/tests/conditionals/cond-wf-003.1_nojs.cwl
@@ -1,5 +1,5 @@
 class: Workflow
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 inputs:
   val:
     type: int

diff --git a/tests/conditionals/cond-wf-003.cwl b/tests/conditionals/cond-wf-003.cwl
@@ -1,5 +1,5 @@
 class: Workflow
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 inputs:
   val: int
   def:

diff --git a/tests/conditionals/cond-wf-003_nojs.cwl b/tests/conditionals/cond-wf-003_nojs.cwl
@@ -1,5 +1,5 @@
 class: Workflow
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 inputs:
   val:
     type: int

diff --git a/tests/conditionals/cond-wf-004.cwl b/tests/conditionals/cond-wf-004.cwl
@@ -1,5 +1,5 @@
 class: Workflow
-cwlVersion: v1.2.0-dev5
+cwlVersion: v1.2
 inputs:
   val: int
   def: