Features to add

[sclayton33]

List of features/enhancements to add:

• If required programs are not installed on the system, install them. Alternatively, create a containerized environment to ship with the pipeline
• Add the option to do transcription factor-enrichment either in the pipeline or as a separate script (potentially use Enrichr or IPA, explore other options)
• Automatically feed the raw counts into a local install of iDEP with pre-defined settings selected prior to running the script and generate figures for all pathways and export lists of all significant expression changes
• Add contaminant checking
• Add BamQC checks
• maybe add rRNA removal even though our sequencing is done with PolyA selection. Maybe add flag --rrna or something to trigger
• add check for 'rename' program installed