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Option to disable filtering

Open grst opened this issue 1 month ago • 2 comments

Description of feature

I would like an option to disable filtering altogether.

My use-case is that I have data that doesn't fall in the filtering scheme provided by the pipeline, because it is centered, and log-transformed data (Continuous values that can be both negative and positive).

Since it's a bit of a special case, I think it's ok that the pipeline doesn't support filtering for these data, and I prefiltered it myself.

I tried setting filtering_min_abundance to -Inf, but it complains because it's not numeric. I now set filtertering_min_abundance to an arbitrary, high negative number (like -100000), but that's obviously not a nice solution.

I think a global --enable_filtering flag that defaults to true would be good. Or, to save parameters, allow setting filtering_min_abundance to null or -Inf.

grst avatar Oct 09 '25 14:10 grst