Merge remote-tracking branch 'origin/master' into directory

Author: mr-c

draft-4/CommandLineTool.yml

@@ -591,6 +591,45 @@ $graph:
         Docker container.
 
 
+- type: record
+  name: SoftwareRequirement
+  extends: "#ProcessRequirement"
+  doc: |
+    Software that should be configured in the environment of the defined
+    process.
+
+    While absolute portability between platforms can be achieved with container
+    technologies like Docker, this mechanism provides an inexact and imprecise
+    fallback. The inexact nature is due to this standard not specifying the
+    base operating environment of the process or how the that environment is to
+    be configured as a result of these hints. The imprecise nature of these
+    hints is due to the `name` and `version` fields being unstructured and not
+    namespaced. The optional `identifier` field is recommended so that users
+    and platforms can distinguish between software that has the same name.
+  fields:
+    - name: spec
+      type:
+        type: array
+        items: SoftwareSpec
+      doc: "The list of software to be configured."
+
+- name: SoftwareSpec
+  type: record
+  fields:
+    - name: name
+      type: string
+      doc: "The name of the software to be configured."
+      jsonldPredicate: "@id"
+    - name: "version"
+      type: string?
+      doc: "The (optional) version of the software to configured."
+    - name: "identifier"
+      type: string?
+      doc: |
+        The (optional) identifier of the software to be configured. Should be a
+        IRI such as an [RRID](http://www.identifiers.org/rrid/SCR_001156).
+        Example: `http://identifiers.org/rrid/RRID:SCR_001156`
+
 - name: DirentExt
   type: record
   doc: |

draft-4/Process.yml

@@ -253,7 +253,29 @@ $graph:
 - name: SchemaBase
   type: record
   abstract: true
+
+
+- name: Parameter
+  type: record
+  extends: "#SchemaBase"
+  abstract: true
+  doc: |
+    Define an input or output parameter to a process.
+
   fields:
+    - name: label
+      type:
+        - "null"
+        - string
+      jsonldPredicate: "rdfs:label"
+      doc: "A short, human-readable label of this parameter object."
+
+    - name: description
+      type:
+        - "null"
+        - string
+      jsonldPredicate: "rdfs:comment"
+      doc: "A long, human-readable description of this parameter object."
     - name: secondaryFiles
       type:
         - "null"
@@ -312,29 +334,6 @@ $graph:
         pipe.  Default: `false`.
 
 
-- name: Parameter
-  type: record
-  extends: "#SchemaBase"
-  abstract: true
-  doc: |
-    Define an input or output parameter to a process.
-
-  fields:
-    - name: label
-      type:
-        - "null"
-        - string
-      jsonldPredicate: "rdfs:label"
-      doc: "A short, human-readable label of this parameter object."
-
-    - name: description
-      type:
-        - "null"
-        - string
-      jsonldPredicate: "rdfs:comment"
-      doc: "A long, human-readable description of this parameter object."
-
-
 - type: enum
   name: Expression
   doc: |

draft-4/Workflow.yml

@@ -255,10 +255,12 @@ $graph:
         the value of the parameter(s) specified in the `source` field, or
         null if there is no `source` field.
 
-        The value of `inputs` in the parameter reference or expression is the
-        input object to the workflow step after assigning the `source` values,
-        but before evaluating any step with `valueFrom`.  The order of
-        evaluating `valueFrom` among step input parameters is undefined.
+        The value of `inputs` in the parameter reference or expression must be
+        the input object to the workflow step after assigning the `source`
+        values and then scattering.  The order of evaluating `valueFrom` among
+        step input parameters is undefined and the result of evaluating
+        `valueFrom` on a parameter must not be visible to evaluation of
+        `valueFrom` on other parameters.
 
 
 - type: record
@@ -502,7 +504,7 @@ $graph:
   extends: ProcessRequirement
   doc: |
     Indicates that the workflow platform must support nested workflows in
-    the `run` field of (WorkflowStep)(#WorkflowStep).
+    the `run` field of [WorkflowStep](#WorkflowStep).
 
 - name: ScatterFeatureRequirement
   type: record

draft-4/conformance_test_draft-4.yaml

@@ -64,6 +64,7 @@
       class: File
       checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
       location:
+      path: Any
       size: 13
   doc: Test command execution in Docker with simplified syntax stdout redirection
 
@@ -88,6 +89,12 @@
   }
   tool: draft-4/egrep-stderr.cwl
   doc: Test command line with stderr redirection
+  output:
+    output_file:
+      class: File
+      checksum: sha1$cec7b8746a78c42060c96505887449bca0142976
+      size: 84
+      path: error.txt
 
 - job:
   output: {
@@ -100,6 +107,12 @@
   }
   tool: draft-4/egrep-stderr-shortcut.cwl
   doc: Test command line with stderr redirection, brief syntax
+  output:
+    output_file:
+      class: File
+      checksum: sha1$cec7b8746a78c42060c96505887449bca0142976
+      size: 84
+      path: Any
 
 - output:
     output_file:
@@ -690,6 +703,12 @@
   tool: "draft-4/scatter-valuefrom-wf4.cwl#main"
   doc: Test workflow scatter with two scatter parameters and dotproduct join method and valueFrom on step input
 
+- job: draft-4/scatter-valuefrom-job1.json
+  output:
+    out: ["foo one one", "foo two two", "foo three three", "foo four four"]
+  tool: draft-4/scatter-valuefrom-wf5.cwl
+  doc: Test workflow scatter with single scatter parameter and valueFrom on step input
+
 - job: draft-4/conflict-job.json
   output: {
     "fileout": {

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

@@ -5,6 +5,8 @@ description: "Print the contents of a file to stdout using 'cat' running in a do
 hints:
   DockerRequirement:
     dockerPull: debian:wheezy
+  SoftwareRequirement:
+    name: cat
 inputs:
   file1:
     type: File

draft-4/draft-4/scatter-valuefrom-wf5.cwl

@@ -0,0 +1,58 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: cwl:draft-4.dev2
+class: Workflow
+inputs:
+  inp:
+    type:
+      type: array
+      items:
+        type: record
+        name: instr
+        fields:
+          - name: instr
+            type: string
+outputs:
+  out:
+    type:
+      type: array
+      items: string
+    outputSource: step1/echo_out
+
+requirements:
+  - class: ScatterFeatureRequirement
+  - class: StepInputExpressionRequirement
+
+steps:
+  step1:
+    in:
+      echo_in:
+        source: inp
+        valueFrom: $(self.instr)
+      first:
+        source: inp
+        valueFrom: $(inputs.echo_in.instr)
+    out: [echo_out]
+    scatter: echo_in
+    run:
+      class: CommandLineTool
+      inputs:
+        first:
+          type: string
+          inputBinding:
+            position: 1
+        echo_in:
+          type: string
+          inputBinding:
+            position: 2
+      outputs:
+        echo_out:
+          type: string
+          outputBinding:
+            glob: "step1_out"
+            loadContents: true
+            outputEval: $(self[0].contents)
+      baseCommand: "echo"
+      arguments:
+        - "-n"
+        - "foo"
+      stdout: "step1_out"