Must include everything that is needed for SPACEMAKE 2.0 (aka drop-dropseq), but also come with sufficient examples & docs to allow others to re-use in other scenarios.
- expanded documentation (split-by UMI or CB tag)
- one round of adding doc-strings and auto-generating reference docs (sphinx?)
Minor improvements in usability and documentation.
- built-in performance/throughput sensors and statistics output to identify bottlenecks
- better workflow representation (as str but also as graph)
- improve documentation
Major new features that may never be needed. Just collecting ideas here.
- support binary I/O in addition to line-based. Might make sense for BAM blocks but the format is pretty hard to break up. Would certainly require hacking HTSlib in ways that make me woozy.
- allow sockets in addition to named pipes and files, to scale beyond a single node
- deeper integration with snakemake (similar concepts in many places)