Failed confirmation test on OSX

common-workflow-language
```
commit 7063fc0ae69221d5de13bec6a4e68d5b947e9b96
Date: Sat Feb 18 00:11:50 2017 +0200
```

cwltool
```
commit 59cdde81e5359b3a7739d9666008c7b77c287c1e
Date: Thu Feb 23 09:28:07 2017 -0500
```

output
```
$ ./run_test.sh RUNNER=/Users/gijs/Work/cwltool/.virtualenv/bin/cwl-runner
--- Running conformance test v1.0 on /Users/gijs/Work/cwltool/.virtualenv/bin/cwl-runner ---
/Users/gijs/Work/cwltool/.virtualenv/bin/cwl-runner 1.0.20170223142807
Test [6/87] The file is hello.txt
Test [18/87] Test failed: /Users/gijs/Work/cwltool/.virtualenv/bin/cwl-runner --tmp-outdir-prefix=/Users/gijs/Work/common-workflow-language/v1.0O6lrnC --tmpdir-prefix=/Users/gijs/Work/common-workflow-language/v1.0O6lrnC --outdir=/Users/gijs/Work/common-workflow-language/v1.0O6lrnC --quiet v1.0/wc-tool.cwl v1.0/wc-job.json
Test command execution in with stdin and stdout redirection
Compare failure expected: {
"output": {
"checksum": "sha1$631bfbac524e2d04cdcc5ec33ade827fc10b06ae",
"class": "File",
"location": "output",
"size": 15
}
}
got: {
"output": {
"basename": "output",
"checksum": "sha1$ae852d273ed56a04c9efd6aaa6f1376d6c03f312",
"class": "File",
"location": "file:///Users/gijs/Work/common-workflow-language/v1.0O6lrnC/output",
"path": "/Users/gijs/Work/common-workflow-language/v1.0O6lrnC/output",
"size": 25
}
}
caused by: failed comparison for key 'output': expected: {
"checksum": "sha1$631bfbac524e2d04cdcc5ec33ade827fc10b06ae",
"class": "File",
"location": "output",
"size": 15
}
got: {
"basename": "output",
"checksum": "sha1$ae852d273ed56a04c9efd6aaa6f1376d6c03f312",
"class": "File",
"location": "file:///Users/gijs/Work/common-workflow-language/v1.0O6lrnC/output",
"path": "/Users/gijs/Work/common-workflow-language/v1.0O6lrnC/output",
"size": 25
}
caused by: field 'checksum' failed comparison: expected: "sha1$631bfbac524e2d04cdcc5ec33ade827fc10b06ae"
got: "sha1$ae852d273ed56a04c9efd6aaa6f1376d6c03f312"
Test [49/87] Hello world!
Test [69/87] x hello.txt
x goodbye.txt
Test [78/87] HOME=/Users/gijs/Work/common-workflow-language/v1.0nwqTQhXPSZc1 TMPDIR=/private/var/folders/qs/hpsrfjwx0313rdk2t7jj2ddw0000gn/T/tmpujWuKT
Test [79/87] HOME=/private/var/spool/cwl TMPDIR=/tmp
[job envvar2.cwl] completed permanentFail
Final process status is permanentFail
Test failed: /Users/gijs/Work/cwltool/.virtualenv/bin/cwl-runner --tmp-outdir-prefix=/Users/gijs/Work/common-workflow-language/v1.0533edw --tmpdir-prefix=/Users/gijs/Work/common-workflow-language/v1.0533edw --outdir=/Users/gijs/Work/common-workflow-language/v1.0533edw --quiet v1.0/envvar2.cwl v1.0/empty.json
Test $HOME and $TMPDIR are set correctly in Docker
Returned non-zero
Test [87/87] 85 tests passed, 2 failures, 0 unsupported features

1 tool tests failed
```