many large revisions for v1.2 release (see Revision History for more details)
major changes:
Documentation/submission_helper.txt
fuzzy demultiplexing barcode match
rearrange order of notebooks to group modalities. i.e., A04+A05 = methylation and A06+A07 = transcriptome (many filepaths changed)
Split bismark & STAR comprehensive mapping steps --> smaller steps for easier cluster scheduling
RNA deduplication --> keeping highest quality alignment
Full Changelog: v1.1.3...v1.2.1