- Clean up `Snakefile` onsuccess commands
- Clean up config files
- Add fallback cluster params for rules potentially needing large amounts of memory
- Update binner env yamls
- Implement COMEBIN with GPU support
- Try to deal with DAS_Tool edge cases better
- Use intermediary updated MetaWrap refinement using CheckM2
- Implement fastp to replace trimmomatic
- Implement Bracken for tax abundance estimation
- Remove some debug prints
- Fix wrong mem-per-core settings for some rules
- Ensure min memory available for some rules failing with large files
- Start implementing experimental gene/contig depth rule changes to deal with high coverage region oom fails (e.g. if rRNAs present)
- Implements Mantis annotation rule retries with progressively more mem-per-core
- Ensure more min memory for prokka
- Use `temp()` directive for more various temporary files
- Increase runtime of various rules running out of time with large samples
- Begin implementation of read coverage normalization option
- Clean up some commented code
- Begin cleanup of archiving of files, only keep final read files etc.
- Fix final bin stats table generation to handle CheckM2 output