Task list for rotary

[jmtsuji]

Can be converted to issues if complex:

Usability / reproducibility:

• Address TODOs in the Snakefiles #156
• Make a proper front-end CLI (see Rotary CLI #23 )
• Add short read QC or at least code in the repo that shows how to do short read QC
• End-to-end test with proper hash comparisons (need to find some deterministic endpoints) Too hard with current CI systems and pipeline size - low priority.
• Install scripts properly (e.g., make the whole thing a pip and/or conda install) so that downloading the release to the downloads folder (in the snakefile) is no longer needed
• Split snakefile into multiple files
• Improve run reports for rotary #157

Low priority:

• Add support for well-parallelized medaka
• Make symlinks of the QC'ed short read at the start to simplify logging #158
• Add option for nano-corr in flye / repair script #159
• Metagenomics Mode (MetaFlye and Binning) #160

[LeeBergstrand]

@jmtsuji Moved to individual issues.

[jmtsuji]

Thanks!