Add test for using initial work dir, docker, and secondary files.

Author: Peter Amstutz

v1.0/conformance_test_v1.0.yaml

@@ -867,3 +867,19 @@
     }
   tool: "v1.0/js-expr-req-wf.cwl#wf"
   doc: Test that expressionLib requirement of individual tool step overrides expressionLib of workflow.
+
+- job: v1.0/initialworkdirrequirement-docker-out-job.json
+  output:
+    OUTPUT:
+      "checksum": "sha1$aeb3d11bdf536511649129f4077d5cda6a324118"
+      "location": "ref.fasta"
+      "secondaryFiles": [{
+        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+        "location": "ref.fasta.fai",
+          "class": "File",
+          "size": 0
+      }]
+      "class": "File"
+      "size": 12010
+  tool: v1.0/initialworkdirrequirement-docker-out.cwl
+  doc: Test output of InitialWorkDir

v1.0/v1.0/initialworkdirrequirement-docker-out-job.json

@@ -0,0 +1,6 @@
+{
+    "INPUT": {
+        "class": "File",
+        "location": "ref.fasta"
+    }
+}

v1.0/v1.0/initialworkdirrequirement-docker-out.cwl

@@ -0,0 +1,30 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+
+requirements:
+  - class: DockerRequirement
+    dockerPull: debian:8
+  - class: InitialWorkDirRequirement
+    listing:
+      - $(inputs.INPUT)
+
+class: CommandLineTool
+
+inputs:
+  - id: INPUT
+    type: File
+
+outputs:
+  - id: OUTPUT
+    type: File
+    outputBinding:
+      glob: $(inputs.INPUT.basename)
+    secondaryFiles:
+      - .fai
+
+arguments:
+  - valueFrom: $(inputs.INPUT.basename).fai
+    position: 0
+
+baseCommand: [touch]