exec of cwl with $include fails

Bug Report

Looks like there is a failure to resolve the path of includes when pulling in linked files to CWL definition.

Project stucture:

dockstore-cgpmap
  - cwls
    - includes
        doc.yml
    - mixins
        hints.yml
        requirements.yml
    cgpmap-bamOut.cwl
    cgpmap-bamOut.cwl

cwl snippet

...
doc:
  $include: includes/doc.yml
...

Expected behaviour

Should build a local structure to mirror above pulling down the relates files before executing cwltool.

Actual behaviour

dockstore tool launch --entry quay.io/wtsicgp/dockstore-cgpmap/cgpmap-bamOut:3.0.0-rc7 --json fastq_gz_input.json 
Error writing to File
java.io.FileNotFoundException: /tmp/1518013364741-0/cwlsincludes/doc.yml (No such file or directory)

Looks like missing / in cwlsincludes. Note that no erroneously named folder was created either.

$ tree /tmp/1518013364741-0
/tmp/1518013364741-0
└── cwls
    └── cgpmap-bamOut.cwl

Steps to reproduce the behaviour

As above

Environment (Browser or OS and Dockstore version)

$ dockstore --version
Dockstore version 1.3.3

[keiranmraine]

I can work around the symlink so it’s not a problem just wanted to highlight that isn’t possible.

[garyluu]

Seems to launch fine alongside https://github.com/ga4gh/dockstore/issues/1149 cgpmap with 3.0.0-rc8