Invalid filename when transferring Directory between steps

@michael-kotliar [commented on 24 Jan 2017](https://github.com/common-workflow-language/common-workflow-language/issues/375#issue-202706861)

> Hi all! Noticed one interesting thing that may cause a problem when running java application in a workflow step.
>
> **Brief explanation:**
> Workflow structure: File -> Step1 -> Directory -> Step2 -> File
> On the input of Step2 I got an error:
> ` WorkflowException("Invalid filename: '%s' contains illegal characters" % (f["basename"]))`
> ` WorkflowException: Invalid filename: '' contains illegal characters`,
> because after Step1 some of the subfolders of Directory have `"basename": ""`
>
> **Detailed explanation:**
> Link on the workflow with all Dockerfiles and input data:
> https://github.com/michael-kotliar/cwl_sandbox/tree/master/fastqc_parser
> If run workflow - get an error:
> `cwl-runner --debug workflow.cwl workflow-job.json`
> If run each tools separately - all works fine:
> `cwl-runner --debug fastqc.cwl fastqc-job.json`
> `cwl-runner --debug parse-fastqc-results.cwl parse-fastqc-results-job.json`
>
> Part of workflow log, where some of the basenames are empty :
> ```
> [job fastqc] completed success
> [job fastqc] {
> "report_dir": {
> "basename": "tmp4m7vzp",
> "listing": [
> {
> "checksum": "sha1$7cccb0555aace9287c0b16ab17f0b9e663cb7cd5",
> "basename": "test_fastqc.html",
> "size": 341364,
> "class": "File",
> "location": "file:///tmp/tmp4m7vzp/test_fastqc.html"
> },
> {
> "basename": "",
> "listing": [
> {
> "basename": "",
> "listing": [
> {
> "basename": "",
> "listing": [
> {
> "basename": "",
> "listing": [
> {
> "checksum": "sha1$a9decdaf8033361823c3fca2714372fbfca5e277",
> "basename": "",
> "size": 7965,
> "class": "File",
> "location": "file:///tmp/tmp4m7vzp/?/.java/fonts/1.7.0_91/fcinfo-1-87028e295b98-Ubuntu-15.10-en.properties"
> }
> ],
> "class": "Directory",
> "location": "file:///tmp/tmp4m7vzp/?/.java/fonts/1.7.0_91"
> }
> ],
> "class": "Directory",
> "location": "file:///tmp/tmp4m7vzp/?/.java/fonts"
> }
> ],
> "class": "Directory",
> "location": "file:///tmp/tmp4m7vzp/?/.java"
> }
> ],
> "class": "Directory",
> "location": "file:///tmp/tmp4m7vzp/?"
> },
> .....
> ```
>
>
>
>