Add optional secondary files to changelog.

Author: Peter Amstutz

CommandLineTool.yml

@@ -75,6 +75,7 @@ $graph:
           input object documents.
         * Clarify behavior of `glob` for absolute paths and symlinks.
         * Clarify behavior of `glob` to include directories.
+        * `secondaryFiles` can now be explicitly marked as `required` or not.
 
       See also the [CWL Workflow Description, v1.1.0-dev1 changelog](Workflow.html#Changelog).
 
@@ -205,7 +206,7 @@ $graph:
         `InputParameter.default` field) must be applied before evaluating the
         expression.
 
-        If the value of the associated input parameter is `null`, `valueFrom` is 
+        If the value of the associated input parameter is `null`, `valueFrom` is
         not evaluated and nothing is added to the command line.
 
         When a binding is part of the `CommandLineTool.arguments` field,
@@ -247,7 +248,7 @@ $graph:
           items: string
       doc: |
         Find files or directories relative to the output directory, using POSIX
-        glob(3) pathname matching.  If an array is provided, find files or 
+        glob(3) pathname matching.  If an array is provided, find files or
         directories that match any pattern in the array.  If an expression is
         provided, the expression must return a string or an array of strings,
         which will then be evaluated as one or more glob patterns.  Must only
@@ -913,14 +914,14 @@ $graph:
     - name: listing
       type:
         - type: array
-          items: 
+          items:
             - "null"
             - File
             - type: array
               items:
                 - File
                 - Directory
-            - Directory 
+            - Directory
             - Dirent
             - string
             - Expression

Process.yml

@@ -501,12 +501,12 @@ $graph:
         it specifies that the following pattern should be applied to the path
         of the primary file to yield a filename relative to the primary File:
 
-          1. If string begins with one or more caret `^` characters, for each
+          1. If string ends with `?` character, remove the last `?` and mark
+            the resulting secondary file as optional.
+          2. If string begins with one or more caret `^` characters, for each
             caret, remove the last file extension from the path (the last
             period `.` and all following characters).  If there are no file
             extensions, the path is unchanged.
-          2. If string ends with `?` character, remove the last `?` and mark
-            the resulting secondary file as optional.
           3. Append the remainder of the string to the end of the file path.
 
     streamable:

Workflow.yml

@@ -68,6 +68,7 @@ $graph:
         * `WorkflowStepInput` now has a `label` field
         * [Addition](#Requirements_and_hints) of `cwl:requirments` field to
           input object documents
+        * `secondaryFiles` can now be explicitly marked as `required` or not.
 
       See also the [CWL Command Line Tool Description, v1.1.0-dev1 changelog](CommandLineTool.html#Changelog).
 
@@ -327,7 +328,7 @@ $graph:
         1. `null` if there is no `source` field
         2. the value of the parameter(s) specified in the `source` field when this
         workflow input parameter **is not** specified in this workflow step's `scatter` field.
-        3. an element of the parameter specified in the `source` field when this workflow input 
+        3. an element of the parameter specified in the `source` field when this workflow input
         parameter **is** specified in this workflow step's `scatter` field.
 
         The value of `inputs` in the parameter reference or expression must be