genome-grist
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[WIP] add rules for protein mapping
This PR introduces rules to allow mapping nucleotide reads to protein references using Paladin.
not functional yet.
Main questions at this point:
- Do we want to just do this when the user selects protein sourmash? Or do we want to enabling running both protein and nucleotide sourmash within the same grist output folder?
-
mostly what I'm getting at here is whether or not we want to include the
moltype
in thegather
output filename, because we expect folks might want to run both moltypes. I know I want to run both, but I'm not sure if this is a general use case.
-
mostly what I'm getting at here is whether or not we want to include the
- Do we want to store proteomes in the same folder as genbank genomes? Or in a separate folder, e.g.
proteomes
?
To do:
- [ ] make checkpoints --> download proteomes work
- [ ] new checkpoint to prodigal proteome if not downloadable
- [ ] try BBMerge, fall back to PEAR read merging if don't like
- [ ] add tests
- [ ] Add reporting and visualization