As discussed in #85, we need a way to warn users if their sample likely contains multiple strains. For now, we decided that we would like to add a warning based on CheckM2 statistics.
Basic idea:
Make a rule in rotary that analyzes the results of CheckM2
Add to the config a threshold where rotary will warn (or maybe fail is better?) if the contamination is above some % (e.g., 25%)
As discussed in #85, we need a way to warn users if their sample likely contains multiple strains. For now, we decided that we would like to add a warning based on CheckM2 statistics.
Basic idea: