common-workflow-language · tetron · Mar 22, 2018 · Mar 22, 2018
diff --git a/v1.0/conformance_test_v1.0.yaml b/v1.0/conformance_test_v1.0.yaml
@@ -1529,7 +1529,7 @@
     "args": []
   }
   tool: v1.0/empty-array-input.cwl
-  doc: "Test that empty array input does not add anything to command line" 
+  doc: "Test that empty array input does not add anything to command line"
   tags: [ required ]
 
 - job: v1.0/empty.json
@@ -1551,3 +1551,47 @@
   tool: v1.0/valueFrom-constant.cwl
   doc: Test valueFrom with constant value overriding provided array inputs
   tags: [ inline_javascript ]
+
+- job: v1.0/new-dir-job.yml
+  output: {
+    "out": {
+        "checksum": "sha1$ada861e58d3ca64224d5b8ded8cd0e1e7f775057",
+        "class": "File",
+        "location": "output.txt",
+        "size": 26
+    },
+    "outdir": {
+        "location": "sample1",
+        "listing": [
+            {
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "location": "sample1.bam",
+                "class": "File",
+                "size": 0
+            },
+            {
+                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+                "location": "sample1.other",
+                "class": "File",
+                "size": 0
+            }
+        ],
+        "class": "Directory"
+    }
+  }
+  tool: v1.0/new-dir.cwl
+  doc: Test returning directory literal in expression for InitialWorkDir listing
+  tags: [ required ]
+
+- job: v1.0/empty.json
+  output: {
+    "out": {
+        "checksum": "sha1$2aae6c35c94fcfb415dbe95f408b9ce91ee846ed",
+        "class": "File",
+        "location": "output.txt",
+        "size": 11
+    }
+  }
+  tool: v1.0/new-file.cwl
+  doc: Test returning file literal in expression for InitialWorkDir listing
+  tags: [ required ]
diff --git a/v1.0/v1.0/bams/sample1.bam b/v1.0/v1.0/bams/sample1.bam
diff --git a/v1.0/v1.0/bams/sample1.other b/v1.0/v1.0/bams/sample1.other
diff --git a/v1.0/v1.0/new-dir-job.yml b/v1.0/v1.0/new-dir-job.yml
@@ -0,0 +1,4 @@
+input:
+  class: Directory
+  location: bams
+#  location: keep:d287705ded77ef04295b906135fad6b8+53
diff --git a/v1.0/v1.0/new-dir.cwl b/v1.0/v1.0/new-dir.cwl
@@ -0,0 +1,33 @@
+cwlVersion: v1.0
+class: CommandLineTool
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing: |
+       ${
+          var samplename = null;
+          var arr = [];
+          var bam = RegExp('.*\\.bam$')
+          for (var i in inputs.input.listing) {
+            if (!(samplename)) {
+              if (inputs.input.listing[i].basename.match(bam)) {
+                samplename = inputs.input.listing[i].basename.split('.')[0];
+              }
+            }
+          }
+          var inputdir = {"class": "Directory",
+                          "basename": samplename,
+                          "listing": inputs.input.listing};
+          arr.push(inputdir)
+          return arr;
+        }
+inputs:
+  input: Directory
+stdout: output.txt
+outputs:
+  out: stdout
+  outdir:
+    type: Directory
+    outputBinding:
+      glob: sample1
+baseCommand: [ls, sample1/]
diff --git a/v1.0/v1.0/new-file.cwl b/v1.0/v1.0/new-file.cwl
@@ -0,0 +1,19 @@
+cwlVersion: v1.0
+class: CommandLineTool
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing: |
+       ${
+          var arr = [];
+          var inputfile = {"class": "File",
+                          "basename": "input.txt",
+                          "contents": "hello world"};
+          arr.push(inputfile);
+          return arr;
+        }
+inputs: []
+stdout: output.txt
+outputs:
+  out: stdout
+baseCommand: [cat, input.txt]