Fixes #193

Author: GlassOfWhiskey

tests/iwd/iwd-passthrough5.cwl

@@ -0,0 +1,17 @@
+class: CommandLineTool
+cwlVersion: v1.2
+doc: Given a directory, emit it unchanged
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - entry: $(inputs.testdir)
+        writable: false
+inputs:
+  testdir:
+    type: Directory
+outputs:
+  testdir:
+    type: Directory
+    outputBinding:
+      glob: $(inputs.testdir.basename)
+baseCommand: "true"

tests/iwd/iwd-subdir-job.yml

@@ -0,0 +1,3 @@
+testdir:
+  class: Directory
+  path: ../testdir

tests/iwd/iwd-subdir-tool.cwl

@@ -0,0 +1,17 @@
+class: CommandLineTool
+cwlVersion: v1.2
+doc: Given an input directory, emit a subdirectory as output
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - entry: $(inputs.testdir)
+        writable: false
+inputs:
+  testdir:
+    type: Directory
+outputs:
+  testdir:
+    type: Directory
+    outputBinding:
+      glob: testdir/c
+baseCommand: "true"

tests/iwd/iwd-subdir-wf.cwl

@@ -0,0 +1,19 @@
+class: Workflow
+cwlVersion: v1.2
+inputs:
+  testdir: Directory
+outputs:
+  out:
+    type: Directory
+    outputSource: step2/testdir
+steps:
+  step1:
+    run: iwd-subdir-tool.cwl
+    in:
+      testdir: testdir
+    out: [testdir]
+  step2:
+    run: iwd-passthrough5.cwl
+    in:
+      testdir: step1/testdir
+    out: [testdir]

tests/iwd/test-index.yaml

@@ -297,3 +297,24 @@
       "checksum": "sha1$57f77b36009332d236b52b4beca77301b503b27c"
       "size": 268866
   tags: [ initial_work_dir, command_line_tool ]
+
+- job: iwd-subdir-job.yml
+  id: iwd-subdir
+  tool: iwd-subdir-wf.cwl
+  doc: "Test emitting a subdirectory from initial workdir"
+  output:
+    "out": {
+        "location": "c",
+        "basename": "c",
+        "class": "Directory",
+        "listing": [
+            {
+                "location": "d",
+                "basename": "d",
+                "class": "File",
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "size": 0
+            }
+        ]
+    }
+  tags: [ initial_work_dir, command_line_tool, workflow ]