--leave-tmpdir doesn't work

Use https://github.com/common-workflow-language/workflows/blob/58d006a14e4e599fdea19fc3cb65a7a04d31b403/tools/bwa-index.cwl

```
(env) michael@dan:~/workflows$ cwltool --debug --leave-tmpdir --no-container tools/bwa-index.cwl --reference_genome workflows/lobSTR/tmp_1.fq
/home/michael/cwltool/env/bin/cwltool 1.0.20160713142504
Parsed job order from command line: {
"blocksize": null,
"reference_genome": {
"class": "File",
"location": "file:///home/michael/workflows/workflows/lobSTR/tmp_1.fq"
},
"id": "tools/bwa-index.cwl",
"algorithm": null,
"job_order": null
}
[job bwa-index.cwl] initializing from file:///home/michael/workflows/tools/bwa-index.cwl
[job bwa-index.cwl] {
"blocksize": null,
"reference_genome": {
"basename": "tmp_1.fq",
"class": "File",
"location": "file:///home/michael/workflows/workflows/lobSTR/tmp_1.fq"
},
"algorithm": null,
"job_order": null
}
[job bwa-index.cwl] path mappings is {
"file:///home/michael/workflows/workflows/lobSTR/tmp_1.fq": [
"/home/michael/workflows/workflows/lobSTR/tmp_1.fq",
"/tmp/tmpYZb5Ev/stg7a2e3e0f-9b84-48a3-9b0b-0c971831f897/tmp_1.fq",
"File"
]
}
[job bwa-index.cwl] command line bindings is [
{
"position": [
-1000000,
0
],
"valueFrom": "bwa"
},
{
"position": [
-1000000,
1
],
"valueFrom": "index"
},
{
"position": [
0,
"algorithm"
],
"prefix": "-a",
"valueFrom": null
},
{
"position": [
0,
"blocksize"
],
"prefix": "-b",
"valueFrom": null
},
{
"position": [
3,
"reference_genome"
],
"valueFrom": {
"basename": "tmp_1.fq",
"nameroot": "tmp_1",
"nameext": ".fq",
"location": "file:///home/michael/workflows/workflows/lobSTR/tmp_1.fq",
"path": "/tmp/tmpYZb5Ev/stg7a2e3e0f-9b84-48a3-9b0b-0c971831f897/tmp_1.fq",
"dirname": "/tmp/tmpYZb5Ev/stg7a2e3e0f-9b84-48a3-9b0b-0c971831f897",
"class": "File"
}
}
]
[job bwa-index.cwl] /tmp/tmpy6_35R$ bwa \
index \
/tmp/tmpYZb5Ev/stg7a2e3e0f-9b84-48a3-9b0b-0c971831f897/tmp_1.fq
Exception while running job
Traceback (most recent call last):
File "/home/michael/cwltool/cwltool/job.py", line 178, in run
self.outdir, separateDirs=False)
File "/home/michael/cwltool/cwltool/pathmapper.py", line 90, in __init__
self.setup(referenced_files, basedir)
File "/home/michael/cwltool/cwltool/pathmapper.py", line 130, in setup
self.visit(fob, stagedir, basedir)
File "/home/michael/cwltool/cwltool/pathmapper.py", line 105, in visit
self.visitlisting(obj.get("listing", []), stagedir, basedir)
File "/home/michael/cwltool/cwltool/pathmapper.py", line 95, in visitlisting
tgt = os.path.join(stagedir, ld["basename"])
TypeError: string indices must be integers, not str
[job bwa-index.cwl] completed permanentFail
[job bwa-index.cwl] {}
Final process status is permanentFail
[job bwa-index.cwl] Removing input staging directory /tmp/tmpYZb5Ev
[job bwa-index.cwl] Removing empty output directory /tmp/tmpy6_35R
Workflow error, try again with --debug for more information:
Process status is ['permanentFail']
Traceback (most recent call last):
File "/home/michael/cwltool/cwltool/main.py", line 707, in main
**vars(args))
File "/home/michael/cwltool/cwltool/main.py", line 218, in single_job_executor
raise WorkflowException(u"Process status is %s" % (final_status))
WorkflowException: Process status is ['permanentFail']
(env) michael@dan:~/workflows$ ls /tmp/tmpy6_35R
ls: cannot access '/tmp/tmpy6_35R': No such file or directory

```