Additional tests on default value at the WorkflowStep level

Author: LanderOtto

conformance_tests.yaml

@@ -1801,6 +1801,30 @@
   doc: Test workflow scatter with single scatter parameter and two valueFrom using $inputs (first and current el)
   tags: [ scatter, step_input, workflow ]
 
+- job: tests/empty.json
+  output: {"result": [
+    {
+      "class": "File",
+      "checksum": "sha1$4bb9bb2748a4380f12c039a9c2268115b816a6de",
+    },
+    {
+      "class": "File",
+      "checksum": "sha1$cf42ecac010c90a72257a573a5ce7efb7d6f0e08",
+    }
+  ]}
+  tool: tests/scatter-defaults.cwl
+  id: scatter_all_input_defaults
+  doc: Test workflow scatter with single scatter parameter and two default inputs
+  tags: [ scatter, workflow ]
+
+- job: tests/bwa-mem-job.json
+  output:
+    out1: [ "foo 1", "foo 2", "foo 3", "foo 4"]
+  tool: tests/scatter-valuefrom-default.cwl
+  id: wf_scatter_valuefrom_default
+  doc: Test workflow scatter with single scatter parameter, a valueFrom in the WorkflowStep and a default value inside the step
+  tags: [ scatter, step_input, workflow ]
+
 - job: tests/import_schema-def_job.yml
   output:
     output_bam:

tests/loop/default-stepinput-loop.cwl

@@ -0,0 +1,47 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.3.0-dev1
+class: Workflow
+requirements:
+  InlineJavascriptRequirement: {}
+  ScatterFeatureRequirement: {}
+  StepInputExpressionRequirement: {}
+  SubworkflowFeatureRequirement: {}
+inputs: []
+outputs:
+  o1:
+    type: int[]
+    outputSource: loop/o1
+    pickValue: all_non_null
+steps:
+  loop:
+    when: $(inputs.i1 < 20)
+    loop:
+      i1:
+        valueFrom: $(inputs.i1 + 5)
+    outputMethod: all_iterations
+    run:
+      class: Workflow
+      inputs:
+        i1: int
+      outputs:
+        o1:
+          type: int?
+          outputSource: big_values/o1
+      steps:
+        big_values:
+          when: $(inputs.i1 >= 5)
+          run:
+            class: ExpressionTool
+            inputs:
+              i1: int
+            outputs:
+              o1: int
+            expression: >
+              ${return {'o1': inputs.i1 + 3};}
+          in:
+            i1: i1
+          out: [ o1 ]
+    in:
+      i1: 
+        default: 5
+    out: [ o1 ]

tests/loop/test-index.yaml

@@ -107,3 +107,12 @@
     o1: [8, 11, 14, 17, 20]
   doc: "Test a loop whose source has a default value"
   tags: [ conditional, loop, inline_javascript, scatter, workflow ]
+
+- job: single-var-loop-job.yml
+  tool: default-stepinput-loop.cwl
+  id: loop_default_stepinput
+  output:
+    o1: [8, 13, 18]
+  doc: "Test a loop whose source has a default value updated by a valueFrom directive"
+  tags: [ conditional, loop, inline_javascript, scatter, workflow ]
+

tests/scatter-defaults.cwl

@@ -0,0 +1,21 @@
+class: Workflow
+cwlVersion: v1.3.0-dev1
+
+requirements:
+  ScatterFeatureRequirement: {}
+  SubworkflowFeatureRequirement: {}
+
+inputs: []
+outputs:
+  result:
+    type: File[]
+    outputSource: step1/result
+
+steps:
+  step1:
+    run: floats_small_and_large_nojs.cwl
+    in: 
+      annotation_prokka_evalue: 
+        default: [0.1, 0.2]
+    out: [ result ]
+    scatter: annotation_prokka_evalue

tests/scatter-valuefrom-default.cwl

@@ -0,0 +1,39 @@
+class: Workflow
+cwlVersion: v1.3.0-dev1
+
+requirements:
+  StepInputExpressionRequirement: {}
+  SubworkflowFeatureRequirement: {}
+  ScatterFeatureRequirement: {}
+  InlineJavascriptRequirement: {}
+
+inputs: 
+  min_std_max_min: int[]
+
+outputs:
+  out1:
+    type: string[]
+    outputSource: step1/out1
+
+steps:
+  step1:
+    run: 
+      class: Workflow
+      inputs: 
+        value: int
+      outputs:
+        out1:
+          type: string
+          outputSource: step2/out1
+      steps:
+        step2:
+          run: conditionals/cond-wf-003_nojs.cwl
+          in: 
+            val: value
+            test: 
+              valueFrom: "$(true)"
+          out: [ out1 ]
+    scatter: value
+    in:
+      value: min_std_max_min
+    out: [out1]