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.
Can you change the error message to say:

**The option otu_picking_method cannot be passed via the parameters file. Instead, pass --otu_picking_method on the command line.**

I tested this locally and it works as expected.