Tidy Input parameters

[andredsim]

Remove rcfiles input parameter, Now users can use reads with either a vector of .bam paths, a vector of .rds paths, or a list of rcfiles (must be RangedSummarizedExperiment, such as outputed when quant and discovery are false) a path to a gtf file can be passed to annotations and will be automatically openeed with a message saying we recommend preparing annotations in advance Fixed a bug that stopped bambu running with multiple rcFiles are input