Make bowtie pre-mapping optional

[CharlotteAnne]

Add flag to rna_align subworkflow to make bowtie premapping optional
flag would need to go in nextflow.config too

[CharlotteAnne]

One other part of the pipeline that will need changed is the prepare_genome subworkflow - this prepares all the genome inputs like indexes .etc but if you don't do the premapping then the bowtie index doesn't need to be made.