Description of feature

Hello,

Would it be possible not to instruct Bismark methylation extractor to use both the --comprehensive and --merge_non_CpG flags when specifying --comprehensive to the pipeline ?

This is not big issue since it is possible to act on it (thank you for your answer on the issue #372 ). However, in plants, the three methylation contexts are (almost) always considered independently in methylome analysis, and I found a little bit confusing to 'only' get "CpG" and "non_CpG" results with the Bismark workflow by using the same flag than the one currently used on Bismark to access CHG and CHH context independently.

I think having an easier way to chose directly in the pipeline if we want 'non_CpG' merged or not when using bismark workflow might be a plus for plant biologists !

Best regards,