update WDL from draft-2 spec to v1.0

[tomkinsc]

The WDL 1.0 spec is now out and supported by Cromwell. The WDL workflows of viral-ngs should be updated to adhere to this spec. Specs:

• https://github.com/openwdl/wdl/blob/master/versions/draft-2/SPEC.md
• https://github.com/openwdl/wdl/blob/master/versions/1.0/SPEC.md

Note that this is dependent on dxWDL supporting WDL 1.0 (as of 7/5/18 only draft-2 is supported). See the dxWDL imports used, and the readme.

Hopefully this will allow for the removal of the hacky validation of WDL files from validate-wdl.sh.

[dpark01]

This is mostly straightforward once dxWDL supports it, but pay particular attention to how dxWDL decides to implement streaming inputs using the new WDL 1.0 way.

[tomkinsc]

dxWDL has been updated to support WDL v1.0, so we can start updating our pipelines.

[dpark01]

Great! One thing I’d like to check on first before we run down this path—what the roadmap is for 1.0 support at Dockstore (I think possibly everything except DAG visualization might work, now that DNAnexus supports 1.0?)

[tomkinsc]

It sounds like Dockstore is still working on support for WDL 1.0.

[dpark01]

Just bumping this one -- both dxWDL and Dockstore currently support WDL 1.0 now.