Revert "Testing commit operation with minor change"

This reverts commit 656d3ac43b8ee7f813adac55bb0472a1a1901cc6.
Cross-project method name compatibility

Fix method names that were not refactored because they reference
another project
Added options to RNA-seq pipeline

Now read bowtie options from config file for mapping to individual
transcript sequences and filtering ribosomal RNAs
Added bowtie options
Added bowtie options to pipeline