Move SS2 Pipeline Documentation to live near Pipeline

[kbergin]

﹍Why:﹍ We decided as a team we would keep our pipeline documentation near the pipeline in a readme. We then moved the Optimus documentation as we wanted (see here)

﹍Where to start:﹍ The SS2 documentation still lives in this wiki page. Let’s move it into a readme.

AC:

• Pipeline docs are moved to next to pipeline in a readme
• Read through the docs and confirm they are still valid - I’m not sure they’ve been updated since 0.2.0. The data portal documentation is more up to date and could be helpful.
• If not added already, add the information about how it supports mouse now, which reference, and link to wdl that generates the mouse reference.

﹍NOTE:﹍ If this becomes more than a “snack”, we’re almost certainly beyond scope.

┆Issue is synchronized with this Jira Dev Task

[kbergin]

➤ Trevyn Langsford commented:

QA: The SS2 pipeline in skylab should have a README.md ( http://README.md ) next to it.

[kbergin]

➤ Nick Barkas commented:

Looks good! Can you please delete the original Wiki?

[kbergin]

Should we keep it but mark it deprecated and say at the top to go to the readme instead? In the future the readmes will be versioned with the pipeline so we’ll have that history. Thoughts?

[kbergin]

➤ Nick Barkas commented:

I think we should delete. It would make sense to deprecate if it was a high profile page. I don’t think anyone knows about it as it is. Perhaps we could delete and add a note with a link to the new location.

[kbergin]

Alright, well Liz will be doing some documentation work/cleanup in the near future so I’ll ask her to clean up what doesn't make sense to keep.