Should we remove individual asset arguments?

[nsheff]

There are really a lot of CLI args here. Should we consider removing these because they are managed by refgenie?

    parser.add_argument("--TSS-name", default=None,
                        dest="TSS_name", type=str,
                        help="file_name of TSS annotation file.")

    parser.add_argument("--pi-tss", default=None,
                        dest="ensembl_tss", type=str,
                        help="file_name of pause index TSS annotation file.")

    parser.add_argument("--pi-body", default=None,
                        dest="ensembl_gene_body", type=str,
                        help="file_name of pause index gene body annotation file.")

    parser.add_argument("--pre-name", default=None,
                        dest="pre_name", type=str,
                        help="file_name of pre-mRNA annotation file.")

    parser.add_argument("--anno-name", default=None,
                        dest="anno_name", type=str,
                        help="file_name of genomic annotation file.")

    parser.add_argument("--exon-name", default=None,
                        dest="exon_name", type=str,
                        help="file_name of exon annotation file.")

    parser.add_argument("--intron-name", default=None,
                        dest="intron_name", type=str,
                        help="file_name of intron annotation file.")

[jpsmith5]

Still not sure which direction we want to go here. I believe you're likely correct, that it's probably superfluous to include these as options with the streamlining of refgenie handling all of these.