Update for indexing
Update for indexing

Picard indexing wasn't working but I can actually index with the Picard
sort command so I'm doing it there. Eventually I'm hoping I can use
STAR to coordinate sort.

cdeboever3/cdpipelines,frazer-lab/pipelines,cdeboever3/cdpipelines,cdeboever3/cdpipelines,frazer-lab/pipelines,frazer-lab/pipelines