This pull request improves the species estimation of proksee assemble. It addresses multiple issues (#21 #22).
Unfortunately, because RefSeq Masher crashes when given small data sets, I was unable to test SpeciesEstimator as much as I would have liked. Additionally, I had to create some exception handling for when RefSeq Masher crashes, so that the program is able to continue with an "Unknown" species. I think a better long term solution is bug fixing RefSeq Masher (https://github.com/phac-nml/refseq_masher/issues/3).
Other notable changes:
.github/workflows/pr.yml needed to be updated because something the old miniconda was doing became depricated
OrganismDetection was replaced with SpeciesEstimator
cmd_assembly output was cleaned up a little bit
Needed to modify exception handling for SKESA. In particular, in some scenarios is assembles nothing but the previous exception wasn't too help. Related tests were replaced.
This pull request improves the species estimation of proksee assemble. It addresses multiple issues (#21 #22).
Unfortunately, because RefSeq Masher crashes when given small data sets, I was unable to test SpeciesEstimator as much as I would have liked. Additionally, I had to create some exception handling for when RefSeq Masher crashes, so that the program is able to continue with an "Unknown" species. I think a better long term solution is bug fixing RefSeq Masher (https://github.com/phac-nml/refseq_masher/issues/3).
Other notable changes: