Use public scripts in WDL repo for demo/examples

[vdauwera]

The scripts provided in https://github.com/broadinstitute/wdl/tree/develop/scripts/broad_dsde_workflows exercise most commonly used features of WDL. It would be great to see a demo/ examples of how the pipeline builder visualizes these or a subset.

[sidoruka]

@vdauwera , we've looked at the scripts you've mentioned and noticed that we experience certain bugs and miss some features,
(e.g. using variables inside scatter/if/while blocks, accessing scatter iteration item).
Most of the problems are also uncovered in the issues created by @jsotobroad
We have started working on this and will add usage/visualization examples to the tutorials and a demo application and as soon as the problems are solved.

[vdauwera]

That's great to hear, thanks.

[sidoruka]

Seems that we've finally managed to fix all issues that blocked us from providing such demo.
As noted in #16 we've tested all scripts from the folder you've provided.

We linked these scripts into a demo application (TOOLS -> BROAD WDL EXAMPLES -> broad_dsde_workflows). Also there are some other WDL scripts from the same repository. You can load workflows visualizations by clicking a wf item as show on the image below.

Could you plese check this on http://pb.opensource.epam.com:10000/?

[sidoruka]

Also now it is possible to load WDLs directly into builder by URL.

1. ?url= option allows to address WDL script by http link:

• Format: http://pb.opensource.epam.com:10000/?url={WDL_LINK}
• Example: ExtractSamHeadersWf_170107.wdl by URL to GITHUB file

2. ?id= option allows to address WDL script that is previously registered to a TOOL LIBRARY:

• Format: http://pb.opensource.epam.com:10000/?id=`{REGISTERED_NAME}`
• Example: ExtractSamHeadersWf_170107 by ID

[jsotobroad]

I looked at the new build ver. 0.3.10-dev.157 and it seems to be doing scattering a little differently than it used. I dont see any connection from the input to the scatter to the scatter box. In the link provided above I would expect to see bam_list connected to input_bam. It also is a little confusing to me to see sub_strip_path and sub_strip_suffix in the same level as input_bam because input_bam is what the scatter is scattering over and the other two are just declarations in the scatter itself.

The url addition is pretty cool too!

[jsotobroad]

It would also be nice if the workflow outputs on the outer right edge were connected to the task output they come from