Tasks for rotary workflow before exiting beta

[jmtsuji]

Fixes:

• [ ] Minor TODOs in the snakefile
• [x] Separate out downloads (Polypolish, HMM) to their own rule(s)
• [x] Centralized DB dir
• [x] Make more files tmp files (e.g., for polypolish)
• [x] Check if logs look okay for compact polypolish rule; if not, split the logs
• [x] Add code in the README or wiki for how to set up databases
• [x] Only keep top dnaA (or other start marker) hit per contig and throw a warning that others were also found
• [x] Add --meta flag option to Flye

Docs:

• [ ] Add example code for how to do short read QC

Usability / reproducibility:

• [ ] **Add better reporting of key stats from pipeline (e.g., reads filtered during QC, assembly performance, circular vs linear contigs, contigs filtered out during coverage filtration, and so on).
• [ ] Consider a way to report versions, even if just a simple text file in the repo
• [ ] Simple end-to-end test that can be run when downloaded

[jmtsuji]

Now that R10 Nanopore sequencing is becoming more common, it could also be nice to have template config files for the hybrid assembly case vs. the standalone long read case. OR build the CLI so that directly editing the config is usually not necessary.

[jmtsuji]

Closing this issue for now -- I think #15 alone is sufficient. I'll move the leftover details there.