test for nested directories and initial workdir requirement (#126)

Co-authored-by: Michael R. Crusoe <[email protected]>

Author: rupertnash

conformance_tests.yaml

@@ -3399,3 +3399,20 @@
 - $import: tests/mixed-versions/test-index.yaml
 - $import: tests/loadContents/test-index.yaml
 - $import: tests/iwd/test-index.yaml
+
+- doc: Nested directories, InitialWorkDirRequirement, and containers work together
+  label: nested_dirs_iwdr_container
+  tool: tests/nested-dirs-iwdr/test.cwl
+  job: tests/empty.json
+  output:
+    final_output:
+      class: Directory
+      basename: my_dir
+      location: Any
+      listing:
+      - class: File
+        basename: my_file
+        location: Any
+        size: 0
+        checksum: sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709
+  tags: [ workflow, initial_work_dir, subworkflow ]

tests/nested-dirs-iwdr/initial_work_dir.cwl

@@ -0,0 +1,23 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: CommandLineTool
+
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entry: $(inputs.my_input)
+        writable: False
+
+baseCommand: 'true'
+
+inputs:
+  my_input:
+    type: Directory
+    inputBinding:
+      position: 1
+
+outputs:
+  my_output:
+    type: Directory
+    outputBinding:
+      glob: $(inputs.my_input.basename)

tests/nested-dirs-iwdr/mkdir.cwl

@@ -0,0 +1,18 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: CommandLineTool
+
+baseCommand: [bash, '-c', 'mkdir "$1" && touch "$1/my_file"', '-']
+
+inputs:
+  my_input:
+    type: string
+    default: my_dir
+    inputBinding:
+      position: 1
+
+outputs:
+  my_output:
+    type: Directory
+    outputBinding:
+        glob: $(inputs.my_input)

tests/nested-dirs-iwdr/test.cwl

@@ -0,0 +1,32 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+
+# Test that nested directories, InitialWorkDirRequirement, containers
+# work correctly together. This is based on a reported problem, see
+# https://github.com/common-workflow-language/common-workflow-language/issues/749
+hints:
+  DockerRequirement:
+    dockerPull: docker.io/bash:4.4
+
+requirements:
+  - class: SubworkflowFeatureRequirement
+
+inputs: []
+
+steps:
+  directory_output_step:
+    run: mkdir.cwl
+    in: []
+    out: [my_output]
+
+  initial_work_dir_step:
+    run: initial_work_dir.cwl
+    in:
+        my_input: directory_output_step/my_output
+    out: [my_output]
+ 
+outputs:
+  final_output:
+    type: Directory
+    outputSource: initial_work_dir_step/my_output