[Nelsonlab-analysis] Updated Workflow Docs

[Brian O'C. <bri...@gm...>]

Hey Guys,

I updated the SeqWare Pipeline workflow documentation today for
version 0.6.2.1, specifically for the variant DB workflow and the
provisioning of query engine databases.  See:

https://secure.genome.ucla.edu/index.php/Sequence_Analysis_Workflow_HOWTO

for the updated information.

Keep in mind there's a little more work for the database provisioning
steps to work, I need to get Bret and/or Jordan's help with that once
I cleanup some old DBs on compute-2-7. I included a TODO list in the
wiki entry for Bret and Jordan:

https://secure.genome.ucla.edu/index.php/Sequence_Analysis_Workflow_HOWTO#Provisioning_database_to_SeqWare_QueryEngine

The important take home point for "power users" (Kevin, Hane, Michael
Clark, Sam, etc) that want to run workflows for alignment, variant
calling, and annotation is to please use the current tagged version
(0.6.2.1).  This way the directions in the wiki and the tools
parameters will match up.  As new version of SeqWare become available
Jordan will coordinate the software release and documentation on this
wiki page and send out an email letting people know it's been updated.

The next item on my plate is finishing the updates to the LIMS.  I'll
send around links to docs in the wiki and the updated LIMS URL when
it's available (first week of April I hope).  At that point I want to
get everyone's help moving the unstructured sample metadata in the
wiki into the LIMS SRA datamodel.  This will make it much easier to
track samples and what we've done to them computationally.

Hope this helps!

--Brian