Error while running bcbio workflow

## Expected Behavior
The workflow should execute successfully creating RO.

## Actual Behavior
Workflow fails with the following error:
`Anonymous file object must have 'contents' and 'basename' fields.`

## Workflow Code

https://github.com/bcbio/test_bcbio_cwl/blob/master/somatic/somatic-workflow/main-somatic.cwl

## Full Traceback
```pytb
(testing) farahk@4180L-142848-M:~/Documents/conformanceTest-CWLProv/test_bcbio_cwl/somatic/somatic-workflow$ cwltool --provenance ROtest main-somatic.cwl main-somatic-samples.json
/Users/farahk/Documents/testing/bin/cwltool 1.0.20180702035104
[provenance] Temporary research object: /var/folders/bs/8fyl2nt50252htp1d2ct1rd1g51vtc/T/tmp0f6876w5
Resolved 'main-somatic.cwl' to 'file:///Users/farahk/Documents/conformanceTest-CWLProv/test_bcbio_cwl/somatic/somatic-workflow/main-somatic.cwl'
[provenance] Added packed workflow: workflow/packed.cwl
steps/alignment_to_rec.cwl:26:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/prep_align_inputs.cwl:26:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/process_alignment.cwl:27:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/process_alignment.cwl:83:3: Unknown hint http://arvados.org/cwl#APIRequirement
steps/merge_split_alignments.cwl:26:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/prep_samples_to_rec.cwl:26:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/prep_samples.cwl:26:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/postprocess_alignment_to_rec.cwl:26:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/postprocess_alignment.cwl:27:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/postprocess_alignment.cwl:54:3: Unknown hint http://arvados.org/cwl#APIRequirement
steps/combine_sample_regions.cwl:27:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/combine_sample_regions.cwl:42:3: Unknown hint http://arvados.org/cwl#APIRequirement
steps/batch_for_variantcall.cwl:26:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/get_parallel_regions.cwl:26:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/variantcall_batch_region.cwl:27:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/variantcall_batch_region.cwl:105:3: Unknown hint http://arvados.org/cwl#APIRequirement
steps/variantcall_batch_region.cwl:106:3: Unknown hint http://arvados.org/cwl#RuntimeConstraints
steps/concat_batch_variantcalls.cwl:27:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/concat_batch_variantcalls.cwl:42:3: Unknown hint http://arvados.org/cwl#APIRequirement
steps/postprocess_variants.cwl:26:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/compare_to_rm.cwl:26:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/summarize_vc.cwl:26:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/qc_to_rec.cwl:26:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/pipeline_summary.cwl:27:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
steps/pipeline_summary.cwl:76:3: Unknown hint http://arvados.org/cwl#RuntimeConstraints
steps/multiqc_summary.cwl:26:3: Unknown hint https://www.dnanexus.com/cwl#InputResourceRequirement
[provenance] Finalizing Research Object
[provenance] Generated bagit metadata: /var/folders/bs/8fyl2nt50252htp1d2ct1rd1g51vtc/T/tmp0f6876w5
[provenance] Deleting existing /Users/farahk/Documents/conformanceTest-CWLProv/test_bcbio_cwl/somatic/somatic-workflow/ROtest
[provenance] Research Object saved to /Users/farahk/Documents/conformanceTest-CWLProv/test_bcbio_cwl/somatic/somatic-workflow/ROtest
Traceback (most recent call last):
File "/Users/farahk/Documents/testing/bin/cwltool", line 11, in
sys.exit(main())
File "/Users/farahk/Documents/testing/lib/python3.6/site-packages/cwltool/main.py", line 574, in main
secret_store=runtimeContext.secret_store)
File "/Users/farahk/Documents/testing/lib/python3.6/site-packages/cwltool/main.py", line 221, in init_job_order
basedir=file_uri(str(input_basedir) + "/"))
File "/Users/farahk/Documents/testing/lib/python3.6/site-packages/cwltool/main.py", line 288, in printdeps
{"$include", "$schemas", "location"}, loadref)
File "/Users/farahk/Documents/testing/lib/python3.6/site-packages/cwltool/process.py", line 933, in scandeps
r.extend(scandeps(base, v, reffields, urlfields, loadref, urljoin=urljoin))
File "/Users/farahk/Documents/testing/lib/python3.6/site-packages/cwltool/process.py", line 936, in scandeps
r.extend(scandeps(base, d, reffields, urlfields, loadref, urljoin=urljoin))
File "/Users/farahk/Documents/testing/lib/python3.6/site-packages/cwltool/process.py", line 939, in scandeps
normalizeFilesDirs(r)
File "/Users/farahk/Documents/testing/lib/python3.6/site-packages/cwltool/pathmapper.py", line 82, in normalizeFilesDirs
visit_class(job, ("File", "Directory"), addLocation)
File "/Users/farahk/Documents/testing/lib/python3.6/site-packages/cwltool/utils.py", line 234, in visit_class
visit_class(d, cls, op)
File "/Users/farahk/Documents/testing/lib/python3.6/site-packages/cwltool/utils.py", line 231, in visit_class
visit_class(rec[d], cls, op)
File "/Users/farahk/Documents/testing/lib/python3.6/site-packages/cwltool/utils.py", line 234, in visit_class
visit_class(d, cls, op)
File "/Users/farahk/Documents/testing/lib/python3.6/site-packages/cwltool/utils.py", line 229, in visit_class
op(rec)
File "/Users/farahk/Documents/testing/lib/python3.6/site-packages/cwltool/pathmapper.py", line 58, in addLocation
raise validate.ValidationException("Anonymous file object must have 'contents' and 'basename' fields.")
schema_salad.validate.ValidationException: Anonymous file object must have 'contents' and 'basename' fields.
```

## Your Environment
* cwltool version:
cwltool 1.0.20180702035104
Mac OS High Sierra