Merge remote-tracking branch 'origin/master' into scatter-inputs

Author: mr-c

draft-4/CommandLineTool.yml

@@ -626,6 +626,44 @@ $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: CreateFileRequirement
   type: record

draft-4/Process.yml

@@ -141,7 +141,29 @@ $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"
@@ -200,29 +222,6 @@ $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

@@ -504,7 +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

@@ -60,6 +60,12 @@
 - job: draft-4/cat-job.json
   tool: draft-4/cat3-tool-shortcut.cwl
   doc: Test command execution in Docker with stdout redirection
+  output:
+    output_file:
+      class: File
+      checksum: sha1$47a013e660d408619d894b20806b1d5086aab03b
+      path: Any
+      size: 13
 
 - job: draft-4/cat-job.json
   output:
@@ -76,11 +82,23 @@
   job:
   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
 
 - args: [egrep]
   job:
   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
 
 - args: [egrep]
   stderr: std.err

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