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 just use the value that you set above here, rather than perform this check again? I think that would be more clear (i.e., so ``if run_step_2_and_3``).