Update conformance tests to use draft-4 syntax improvements.

Author: Peter Amstutz

draft-4/Workflow.yml

@@ -441,7 +441,8 @@ $graph:
       type:
         - type: array
           items: "#WorkflowStep"
-
+      jsonldPredicate:
+          mapSubject: id
 
 
 - type: record

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

@@ -4,11 +4,11 @@ class: CommandLineTool
 cwlVersion: cwl:draft-4.dev1
 
 inputs:
-  - id: reference
+  reference:
     type: File
     inputBinding: { position: 2 }
 
-  - id: reads
+  reads:
     type:
       type: array
       items: File

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

@@ -5,37 +5,37 @@ cwlVersion: cwl:draft-4.dev1
 class: CommandLineTool
 
 hints:
-  - class: DockerRequirement
+  DockerRequirement:
     dockerPull: images.sbgenomics.com/rabix/bwa
     dockerImageId: 9d3b9b0359cf
 
-  - class: ResourceRequirement
+  ResourceRequirement:
     coresMin: 4
 
 inputs:
-  - id: reference
+  reference:
     type: File
     inputBinding: { position: 2 }
 
-  - id: reads
+  reads:
     type:
       type: array
       items: File
     inputBinding: { position: 3 }
 
-  - id: minimum_seed_length
+  minimum_seed_length:
     type: int
     inputBinding: { position: 1, prefix: -m }
 
-  - id: min_std_max_min
+  min_std_max_min:
     type: { type: array, items: int }
     inputBinding:
       position: 1
       prefix: -I
       itemSeparator: ","
 
 outputs:
-  - id: sam
+  sam:
     type: File
     outputBinding: { glob: output.sam }
 

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

@@ -3,13 +3,13 @@ cwlVersion: cwl:draft-4.dev1
 class: CommandLineTool
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
-  - class: DockerRequirement
+  DockerRequirement:
     dockerPull: debian:wheezy
 inputs:
-  - id: file1
+  file1:
     type: File
     inputBinding: {position: 1}
-  - id: numbering
+  numbering:
     type: ["null", boolean]
     inputBinding:
       position: 0

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

@@ -3,10 +3,10 @@ class: CommandLineTool
 cwlVersion: cwl:draft-4.dev1
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
-  - class: DockerRequirement
+  DockerRequirement:
     dockerPull: debian:wheezy
 inputs:
-  - id: file1
+  file1:
     type: File
 outputs: []
 baseCommand: cat

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

@@ -3,16 +3,16 @@ class: CommandLineTool
 cwlVersion: cwl:draft-4.dev1
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
-  - class: DockerRequirement
+  DockerRequirement:
     dockerPull: debian:wheezy
 inputs:
-  - id: file1
+  file1:
     type: File
     label: Input File
     description: "The file that will be copied using 'cat'"
     inputBinding: {position: 1}
 outputs:
-  - id: output_file
+  output_file:
     type: File
     outputBinding: {glob: output.txt}
 baseCommand: cat

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

@@ -3,13 +3,13 @@ class: CommandLineTool
 cwlVersion: cwl:draft-4.dev1
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
-  - class: DockerRequirement
+  DockerRequirement:
     dockerPull: debian:wheezy
 inputs:
-  - id: file1
+  file1:
     type: File
 outputs:
-  - id: output_txt
+  output_txt:
     type: File
     outputBinding:
       glob: output.txt

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

@@ -3,18 +3,18 @@ cwlVersion: cwl:draft-4.dev1
 class: CommandLineTool
 description: "Print the contents of a file to stdout using 'cat' running in a docker container."
 hints:
-  - class: DockerRequirement
+  DockerRequirement:
     dockerPull: "debian:wheezy"
-  - class: BlibberBlubberFakeRequirement
+  BlibberBlubberFakeRequirement:
     fakeField: fraggleFroogle
 inputs:
-  - id: file1
+  file1:
     type: File
     label: "Input File"
     description: "The file that will be copied using 'cat'"
     inputBinding: {position: 1}
 outputs:
-  - id: output_file
+  output_file:
     type: File
     outputBinding: {glob: output.txt}
 baseCommand: cat

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

@@ -1,35 +1,35 @@
 cwlVersion: cwl:draft-4.dev1
 $graph:
-- class: CommandLineTool
-  id: echo
+- id: echo
+  class: CommandLineTool
   inputs:
-    - id: text
+    text:
       type: string
       inputBinding: {}
 
   outputs:
-    - id: fileout
+    fileout:
       type: File
       outputBinding:
         glob: out.txt
 
   baseCommand: echo
   stdout: out.txt
 
-- class: CommandLineTool
-  id: cat
+- id: cat
+  class: CommandLineTool
   inputs:
-    - id: file1
+    file1:
       type: File
       inputBinding:
         position: 1
-    - id: file2
+    file2:
       type: File
       inputBinding:
         position: 2
 
   outputs:
-    - id: fileout
+    fileout:
       type: File
       outputBinding:
         glob: out.txt
@@ -41,40 +41,35 @@ $graph:
   id: collision
 
   inputs:
-    - id: input_1
+    input_1:
       type: string
 
-    - id: input_2
+    input_2:
       type: string
 
   outputs:
-    - id: fileout
+    fileout:
       type: File
       source: "#collision/cat_step/fileout"
 
   steps:
-    - id: echo_1
+    echo_1:
       run: "#echo"
-      inputs:
-        - id: text
-          source: "#collision/input_1"
-      outputs:
-        - id: fileout
+      in:
+        text: "#collision/input_1"
+      out: [fileout]
 
-    - id: echo_2
+    echo_2:
       run: "#echo"
-      inputs:
-        - id: text
-          source: "#collision/input_2"
-      outputs:
-        - id: fileout
+      in:
+        text: "#collision/input_2"
+      out: [fileout]
 
-    - id: cat_step
+    cat_step:
       run: "#cat"
-      inputs:
-        - id: file1
+      in:
+        file1:
           source: "#collision/echo_1/fileout"
-        - id: file2
+        file2:
           source: "#collision/echo_2/fileout"
-      outputs:
-        - id: fileout
+      out: [fileout]

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

@@ -3,24 +3,23 @@ class: Workflow
 cwlVersion: cwl:draft-4.dev1
 
 inputs:
-  - { id: file1, type: File }
+  file1:
+    type: File
 
 outputs:
-  - id: count_output
+  count_output:
     type: int
     source: "#step2/output"
 
 steps:
-  - id: step1
+  step1:
     run: wc-tool.cwl
-    inputs:
-      - {id: file1, source: "#file1"}
-    outputs:
-      - {id: output}
+    in:
+      file1: "#file1"
+    out: [output]
 
-  - id: step2
+  step2:
     run: parseInt-tool.cwl
-    inputs:
-      - {id: file1, source: "#step1/output"}
-    outputs:
-      - {id: output}
+    in:
+      file1: "#step1/output"
+    out: [output]

draft-4/draft-4/count-lines2-wf.cwl

@@ -2,40 +2,50 @@
 class: Workflow
 cwlVersion: cwl:draft-4.dev1
 requirements:
-  - class: InlineJavascriptRequirement
+  InlineJavascriptRequirement: {}
 
 inputs:
-    - { id: file1, type: File }
+    file1:
+      type: File
 
 outputs:
-    - { id: count_output, type: int, source: "#step2/parseInt_output"}
+    count_output:
+      type: int
+      source: "#step2/parseInt_output"
 
 steps:
-  - id: step1
-    inputs:
-      - { id: wc_file1, source: "#file1" }
-    outputs:
-      - { id: wc_output }
+  step1:
+    in:
+      wc_file1:
+        source: "#file1"
+    out: [wc_output]
     run:
       id: wc
       class: CommandLineTool
       inputs:
-        - { id: wc_file1, type: File, inputBinding: {} }
+        wc_file1:
+          type: File
+          inputBinding: {}
       outputs:
-        - { id: wc_output, type: File, outputBinding: { glob: output.txt } }
+        wc_output:
+          type: File
+          outputBinding:
+            glob: output.txt
       stdout: output.txt
       baseCommand: wc
 
-  - id: step2
-    inputs:
-      - { id: parseInt_file1, source: "#step1/wc_output" }
-    outputs:
-      - { id: parseInt_output }
+  step2:
+    in:
+      parseInt_file1: "#step1/wc_output"
+    out: [parseInt_output]
     run:
       class: ExpressionTool
       inputs:
-        - { id: parseInt_file1, type: File, inputBinding: { loadContents: true } }
+        parseInt_file1:
+          type: File
+          inputBinding: { loadContents: true }
       outputs:
-        - { id: parseInt_output, type: int }
+        parseInt_output:
+          type: int
       expression: >
         ${return {'parseInt_output': parseInt(inputs.parseInt_file1.contents)};}

draft-4/draft-4/count-lines3-wf.cwl

@@ -3,23 +3,21 @@ class: Workflow
 cwlVersion: cwl:draft-4.dev1
 
 inputs:
-    - id: file1
+    file1:
       type: { type: array, items: File }
 
 outputs:
-    - id: count_output
+    count_output:
       type: { type: array, items: int }
       source: "#step1/output"
 
 requirements:
-  - class: ScatterFeatureRequirement
+  ScatterFeatureRequirement: {}
 
 steps:
-  - id: step1
+  step1:
     run: wc2-tool.cwl
     scatter: "#step1/file1"
-    inputs:
-      - id: file1
-        source: "#file1"
-    outputs:
-      - id: output
+    in:
+      file1: "#file1"
+    out: [output]