Updating to draft-4.dev2

Author: Peter Amstutz

draft-4/Process.yml

@@ -32,6 +32,7 @@ $graph:
     - cwl:draft-3.dev5
     - cwl:draft-3
     - cwl:draft-4.dev1
+    - cwl:draft-4.dev2
 
 - name: CWLType
   type: enum

draft-4/draft-4/binding-test.cwl

@@ -1,7 +1,7 @@
 #!/usr/bin/env cwl-runner
 
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 
 inputs:
   reference:

draft-4/draft-4/bwa-mem-tool.cwl

@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 
 class: CommandLineTool
 

draft-4/draft-4/cat1-tool.cwl

@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 class: CommandLineTool
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
@@ -10,7 +10,7 @@ inputs:
     type: File
     inputBinding: {position: 1}
   numbering:
-    type: ["null", boolean]
+    type: boolean?
     inputBinding:
       position: 0
       prefix: -n

draft-4/draft-4/cat2-tool.cwl

@@ -1,13 +1,12 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   DockerRequirement:
     dockerPull: debian:wheezy
 inputs:
-  file1:
-    type: File
+  file1: File
 outputs: []
 baseCommand: cat
 stdin: $(inputs.file1.path)

draft-4/draft-4/cat3-tool.cwl

@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   DockerRequirement:

draft-4/draft-4/cat4-tool.cwl

@@ -1,13 +1,12 @@
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
   DockerRequirement:
     dockerPull: debian:wheezy
 inputs:
-  file1:
-    type: File
+  file1: File
 outputs:
   output_txt:
     type: File

draft-4/draft-4/cat5-tool.cwl

@@ -1,5 +1,5 @@
 #!/usr/bin/env cwl-runner
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 class: CommandLineTool
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:

draft-4/draft-4/conflict-wf.cwl

@@ -1,4 +1,4 @@
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 $graph:
 - id: echo
   class: CommandLineTool
@@ -41,35 +41,32 @@ $graph:
   id: collision
 
   inputs:
-    input_1:
-      type: string
-
-    input_2:
-      type: string
+    input_1: string
+    input_2: string
 
   outputs:
     fileout:
       type: File
-      source: "#collision/cat_step/fileout"
+      outputSource: cat_step/fileout
 
   steps:
     echo_1:
       run: "#echo"
       in:
-        text: "#collision/input_1"
+        text: input_1
       out: [fileout]
 
     echo_2:
       run: "#echo"
       in:
-        text: "#collision/input_2"
+        text: input_2
       out: [fileout]
 
     cat_step:
       run: "#cat"
       in:
         file1:
-          source: "#collision/echo_1/fileout"
+          source: echo_1/fileout
         file2:
-          source: "#collision/echo_2/fileout"
+          source: echo_2/fileout
       out: [fileout]

draft-4/draft-4/count-lines1-wf.cwl

@@ -1,6 +1,6 @@
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: cwl:draft-4.dev1
+cwlVersion: cwl:draft-4.dev2
 
 inputs:
   file1:
@@ -9,7 +9,7 @@ inputs:
 outputs:
   count_output:
     type: int
-    source: "#step2/output"
+    source: step2/output
 
 steps:
   step1: