Thanks for the suggestion @emescioglu! Keeping the functionality in
filter-features separate has been rather intentional —
filter-samples should not silently drop zero-abundance features, and
filter-features should not silently drop empty samples. We have had similar discussions in the past (and just rehashed this discussion based on your suggestion) but the consensus has generally been that these filtering functions should be kept separate; adding a
--p-min-samples parameter would really just duplicate some functionality from
Having zero-abundance features in a feature table is not necessarily a problem, either. Of course it is “dead weight” especially when running something like ANCOM but we do have tutorials for
filter-features and recommendations elsewhere in the qiime2 documentation that should make these concepts (and the motivations for removing low-abundance features) reasonably clear.
That said, we are here to serve the needs of users — this is the first time we have been asked for this feature but if we get more requests from users, we can get the wheels in motion to add such a parameter.
I hope that makes sense! Thanks for the suggestion.