create a generic bowtie script to store common parameters
create a generic bowtie script to store common parameters

- rather than recycling bowtie shell script, create one that can
  preserve commonly used commands
- just a wapper for bowtie2
- provides a consistant interface that can be used for scripts for other aligners
- needs a separate script to manage the job submission

dpastling/plethora,dpastling/plethora,dpastling/cnv_pipeline,dpastling/plethora,dpastling/cnv_pipeline