Is your feature request related to a problem? Please describe.
Currently, binning by metabat2 is performed on a sample-by-sample basis. Some use cases would benefit from binning across all the samples. This seems to also be supported by (at least some) other binners (like SemiBin 2).
Describe the solution you'd like
We should introduce a flag on the binning action (for all the binners that support it), allowing binning across many samples. The code will need to be updated to accommodate this change.
Open questions
Are there any other changes need to make this happen?
We probably need to combine all the contigs into a single file - this should be possible since the contigs have unique IDs. Should this simply happen within the binning action?
Is your feature request related to a problem? Please describe.
Currently, binning by metabat2 is performed on a sample-by-sample basis. Some use cases would benefit from binning across all the samples. This seems to also be supported by (at least some) other binners (like SemiBin 2).
Describe the solution you'd like
We should introduce a flag on the binning action (for all the binners that support it), allowing binning across many samples. The code will need to be updated to accommodate this change.
Open questions
Are there any other changes need to make this happen?
We probably need to combine all the contigs into a single file - this should be possible since the contigs have unique IDs. Should this simply happen within the binning action?