From 54e67b6d699d804256d018b0f9995b1a8d6e81fa Mon Sep 17 00:00:00 2001
From: bogdang989 <bogdan.gavrilovic@sbgenomics.com>
Date: Tue, 13 Aug 2019 17:19:24 +0200
Subject: [PATCH 1/2] Add test for argument with empty prefix and separate
 false

---
 conformance_tests.yaml                    | 10 ++++++++++
 tests/arg-empty-prefix-separate-false.cwl | 16 ++++++++++++++++
 2 files changed, 26 insertions(+)
 create mode 100644 tests/arg-empty-prefix-separate-false.cwl

diff --git a/conformance_tests.yaml b/conformance_tests.yaml
index 35ac083..b3599e3 100644
--- a/conformance_tests.yaml
+++ b/conformance_tests.yaml
@@ -3313,3 +3313,13 @@
     Test that optional number output is returned as 0, not null
   tags: [ required, inline_javascript, command_line_tool ]
   id: 253
+
+- tool: tests/arg-empty-prefix-separate-false.cwl
+  job: tests/empty.json
+  output: {}
+  label: argument_empty_prefix_separate_false
+  doc: |
+    Test that argument with empty string as prefix and separate 
+    false is not omitted from command line
+  tags: [ required, shell_command, command_line_tool ]
+  id: 254
diff --git a/tests/arg-empty-prefix-separate-false.cwl b/tests/arg-empty-prefix-separate-false.cwl
new file mode 100644
index 0000000..745be67
--- /dev/null
+++ b/tests/arg-empty-prefix-separate-false.cwl
@@ -0,0 +1,16 @@
+class: CommandLineTool
+cwlVersion: v1.1
+baseCommand: []
+inputs: []
+outputs: []
+arguments:
+- position: 1
+  shellQuote: false
+  valueFrom: "non_existing_app"
+- position: 0
+  prefix: ''
+  separate: false
+  shellQuote: false
+  valueFrom: "echo"
+requirements:
+- class: ShellCommandRequirement

From 34bf15eebf0e7e8a9f8006b3a71c64011d85c68b Mon Sep 17 00:00:00 2001
From: bogdang989 <bogdan.gavrilovic@sbgenomics.com>
Date: Wed, 14 Aug 2019 11:45:17 +0200
Subject: [PATCH 2/2] Test 254 - redirect echo to stdout

---
 conformance_tests.yaml                    | 7 ++++++-
 tests/arg-empty-prefix-separate-false.cwl | 7 ++++++-
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/conformance_tests.yaml b/conformance_tests.yaml
index b3599e3..aa2baf2 100644
--- a/conformance_tests.yaml
+++ b/conformance_tests.yaml
@@ -3316,7 +3316,12 @@
 
 - tool: tests/arg-empty-prefix-separate-false.cwl
   job: tests/empty.json
-  output: {}
+  output:
+    "out": {
+        "class": "File",
+        "checksum": "sha1$e1511352b3bd8c37082021bdc5c50ec8e0e3e8db",
+        "size": 17
+    }
   label: argument_empty_prefix_separate_false
   doc: |
     Test that argument with empty string as prefix and separate 
diff --git a/tests/arg-empty-prefix-separate-false.cwl b/tests/arg-empty-prefix-separate-false.cwl
index 745be67..f3acf15 100644
--- a/tests/arg-empty-prefix-separate-false.cwl
+++ b/tests/arg-empty-prefix-separate-false.cwl
@@ -2,7 +2,11 @@ class: CommandLineTool
 cwlVersion: v1.1
 baseCommand: []
 inputs: []
-outputs: []
+outputs: 
+  out:
+    type: File
+    outputBinding:
+      glob: out
 arguments:
 - position: 1
   shellQuote: false
@@ -12,5 +16,6 @@ arguments:
   separate: false
   shellQuote: false
   valueFrom: "echo"
+stdout: out
 requirements:
 - class: ShellCommandRequirement