skipping metabat

[wwood]

Using metabat is generally a good idea because it is fast and often gives useful bins, but I'm confused by the help:

--skip-binners.... # N.B. specifying "metabat" will skip both MetaBAT1 and MetaBAT2.

But then the inputs for das_tool:

rule das_tool:
    input:
...
        metabat_sspec = [] if "metabat_sspec" in config["skip_binners"] else "data/metabat_bins_sspec/done",
        metabat_spec = [] if "metabat_spec" in config["skip_binners"] else "data/metabat_bins_spec/done",
        metabat_ssens = [] if "metabat_ssens" in config["skip_binners"] else "data/metabat_bins_ssens/done",
        metabat_sense = [] if "metabat_sens" in config["skip_binners"] else "data/metabat_bins_sens/done",

Shouldn't it be something along the lines of

metabat_sspec = [] if "metabat_sspec" in config["skip_binners"] or 'metabat' in config['skip_binners'] else "data/metabat_bins_sspec/done",
...

?

[rhysnewell]

It should be, but looks that functionality didn't survive the refactoring that was done. It will get added back in

[wwood]

Oh maybe I misunderstoosd. I think that get converted into this kind of config with each specified:

skip_binners:
- concoct
- rosella
- vamb
- metabat_sens
- metabat_ssens
- metabat_spec
- metabat_sspec
- metabat2

So I think nothing to see here.