Error collecting output for singularity jobs

## Expected Behavior
Tell us what should happen
```
[job tar.cwl] completed success
{
"example_out": {
"checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
"basename": "hello.txt",
"location": "file:///home/user/cwl/hello.txt",
"path": "/home/user/cwl/hello.txt",
"class": "File",
"size": 0
}
}
Final process status is success
```
## Actual Behavior
```
[job tar.cwl] Job error:
Error collecting output for parameter 'example_out':
tar.cwl:18:7: Did not find output file with glob pattern: '['hello.txt']'
[job tar.cwl] completed permanentFail
{}
Final process status is permanentFail
```

## Workflow Code
Basically the tar output example [from here](https://www.commonwl.org/user_guide/04-output/) with added
```
hints:
DockerRequirement:
dockerPull: alpine
```
and executed with `cwl-runner --singularity --debug tar.cwl tar-job.yml`. Full cwl and yml see
[tar.cwl.txt](https://github.com/common-workflow-language/cwltool/files/2833147/tar.cwl.txt)
[tar-job.yml.txt](https://github.com/common-workflow-language/cwltool/files/2833148/tar-job.yml.txt)
attachment.

## Full Traceback
```pytb
[job tar.cwl] Job error:
Error collecting output for parameter 'example_out':
tar.cwl:15:3: Traceback (most recent call last):
tar.cwl:15:3:
tar.cwl:15:3: File "/home/walzer/.local/lib/python2.7/site-packages/cwltool/command_line_tool.py", line 601, in collect_output_ports
tar.cwl:15:3: compute_checksum=compute_checksum)
tar.cwl:15:3:
tar.cwl:15:3: File "/home/walzer/.local/lib/python2.7/site-packages/cwltool/command_line_tool.py", line 724, in collect_output
tar.cwl:15:3: raise WorkflowException("Did not find output file with glob pattern: '{}'".format(globpatterns))
tar.cwl:15:3:
tar.cwl:15:3: File "/home/walzer/.local/lib/python2.7/site-packages/schema_salad/sourceline.py", line 166, in __exit__
tar.cwl:15:3: raise self.makeError("\n".join(traceback.format_exception(exc_type, exc_value, tb)))
tar.cwl:15:3:
WorkflowException: tar.cwl:18:7: Traceback (most recent call last):
tar.cwl:18:7:
tar.cwl:18:7: File "/home/walzer/.local/lib/python2.7/site-packages/cwltool/command_line_tool.py", line 724, in collect_output
tar.cwl:18:7: raise WorkflowException("Did not find output file with glob pattern: '{}'".format(globpatterns))
tar.cwl:18:7:
tar.cwl:18:7: WorkflowException: Did not find output file with glob pattern: '['hello.txt']'
[job tar.cwl] completed permanentFail
[job tar.cwl] {}
[job tar.cwl] Removing input staging directory /tmp/tmpmec2oX
[job tar.cwl] Removing temporary directory /tmp/tmpqopYfp
Removing intermediate output directory /tmp/tmpWY1AEI
```
## Your Environment
* cwltool version:
1.0.20180820141117