parallel pick otus sortmerna

1. Added parallel_pick_otus_sortmerna.py and modified related closed-ref and open-ref pipelines to include this option,

2. Updated index building code to build index within the output directory, rather than tmp directory, in order to avoid over writing index by two separate calls to indexdb_rna.
There is a lot of duplicated code in here, which is not a good way to do this. Isn't it possible to not duplicate this, but just set a few variables differently if we're skipping steps 2 and 3?