missing dependencies csvtk, rapidnj, cgmlst-dists, and scikit-learn.

[russellsmithies]

After a bit of work I have a conda env that works with coreugate. There were a few undocumented dependencies so I thought I'd share my build for others who want to try it.
The main issues were a change in chewbbaca where they removed the --fr argument in v3.0.0, and missing csvtk, rapidnj, cgmlst-dists, and scikit-learn. I'm building the conda env inside a singularity container but this should work for standard conda/mamba as well.

conda create --yes --quiet --name coreugate_2.0.5 -c conda-forge -c anaconda -c bioconda  'nextflow>=20.10' bcftools=1.15.1 singularity 'python>=3.7' 'biopython>=1.70' 'chewbbaca>=2.8.4, <3.0.0' csvtk rapidnj cgmlst-dists scikit-learn

conda activate coreugate_2.0.5

#  use commit 89f613e9984c4d59400ec91d9065a786ddd256dd as there's a println bug in v2.0.5
python3 -mpip install git+https://github.com/kristyhoran/Coreugate.git@89f613e9984c4d59400ec91d9065a786ddd256dd