Optional secondaryFiles

Author: Peter Amstutz

Process.yml

@@ -237,7 +237,9 @@ $graph:
         - "null"
         - type: array
           items: [File, Directory]
-      jsonldPredicate: "cwl:secondaryFiles"
+      jsonldPredicate:
+        _id: "cwl:secondaryFiles"
+        secondaryFilesDSL: true
       doc: |
         A list of additional files or directories that are associated with the
         primary file and must be transferred alongside the primary file.
@@ -458,12 +460,12 @@ $graph:
     secondaryFiles:
       type:
         - "null"
-        - string
-        - Expression
         - SecondaryFileSchema
         - type: array
-          items: [string, Expression, SecondaryFileSchema, "null"]
-      jsonldPredicate: "cwl:secondaryFiles"
+          items: SecondaryFileSchema
+      jsonldPredicate:
+        _id: "cwl:secondaryFiles"
+        secondaryFilesDSL: true
       doc: |
         Only valid when `type: File` or is an array of `items: File`.
 
@@ -902,7 +904,7 @@ $graph:
             the resulting secondary file as optional.
           3. Append the remainder of the string to the end of the file path.
     - name: required
-      type: boolean?
+      type: ["null", boolean, string, Expression]
       doc: |
         An implementation must not fail workflow execution if `required` is
         set to `false` and the expected secondary file does not exist.

conformance_tests.yaml

@@ -1369,6 +1369,14 @@
   doc: Test required, optional and null secondaryFiles on array of files.
   tags: [ docker, inline_javascript, shell_command, command_line_tool ]
 
+- job: tests/docker-array-secondaryfiles-job2.json
+  should_fail: true
+  tool: tests/docker-array-secondaryfiles.cwl
+  label: filesarray_secondaryfiles2
+  id: 100
+  doc: Test required, optional and null secondaryFiles on array of files.
+  tags: [ docker, inline_javascript, shell_command, command_line_tool ]
+
 - job: tests/dir7.yml
   output: {
     "dir": {

tests/docker-array-secondaryfiles-job2.json

@@ -0,0 +1,13 @@
+{
+    "fasta_path": [
+        {
+            "class": "File",
+            "location": "ref.fasta"
+        },
+        {
+            "class": "File",
+            "location": "ref2.fasta"
+        }
+    ],
+    "require_dat": true
+}

tests/docker-array-secondaryfiles.cwl

@@ -21,8 +21,11 @@ inputs:
       - pattern: .crai
         required: false
       - .bai?
-      - pattern: "${ return null }"
-
+      - "${ if (inputs.require_dat) {return '.dat'} else {return null} }"
+      - "${ return null; }"
+      - pattern: .dat2
+        required: $(inputs.require_dat)
+  require_dat: boolean?
 
 outputs:
   bai_list: