Merge pull request #212 from common-workflow-language/cwl-runner-interface

Initial description of cwl-runner interface

Author: mr-c

draft-3/cwl-runner.cwl

@@ -0,0 +1,78 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: "cwl:draft-3"
+
+description: |
+ Generic interface to run a Common Workflow Language tool or workflow from the
+ command line. To be implemented by each CWL compliant execution platform for
+ testing conformance to the standard and optionally for use by users.
+
+inputs:
+ - id: outdir
+   type: string
+   default: outdir
+   description: |
+    Output directory, defaults to the current directory
+   inputBinding:
+    prefix: "--outdir"
+
+ - id: quiet
+   type: boolean
+   description: no diagnostic output
+   inputBinding:
+    prefix: "--quiet"
+
+ - id: toolfile
+   type: [ "null", File ]
+   description: |
+    The tool or workflow description to run. Optional if the jobfile has a
+    `cwl:tool` field to indicate the tool or workflow description to run.
+   inputBinding:
+    position: 1
+
+ - id: jobfile
+   type: File
+   inputBinding:
+    position: 2
+
+ - id: conformance-test
+   type: boolean
+   inputBinding:
+    prefix: "--conformance-test"
+
+ - id: basedir
+   type: string
+   inputBinding:
+    prefix: "--basedir"
+
+ - id: no-container
+   type: boolean
+   description: |
+    Do not execute jobs in a Docker container, even when listed as a Requirement
+   inputBinding:
+    prefix: "--no-container"
+
+ - id: tmp-outdir-prefix
+   type: string
+   description: |
+    Path prefix for temporary directories. Useful for OS X so that boot2docker
+    writes to /Users
+   inputBinding:
+    prefix: "--tmp-outdir-prefix"
+
+ - id: tmpdir-prefix
+   type: string
+   description: |
+    Path prefix for temporary directories
+   inputBinding:
+    prefix: "--tmpdir-prefix"
+
+baseCommand: cwl-runner
+
+stdout: output-object.json
+
+outputs:
+ - id: output-object
+   type: File
+   outputBinding:
+     glob: output-object.json