FIX: correctly import logger

FIX: multiple main() arguments, logging

FIX: create good_id prior to ref in make_file_for_subsample()

Dockerfile

feat: get_abundance_post_collapse now takes group_file arguement

perf: stop err_correct_w_genome from spamming the log

Merge branch 'main' of github.com:milescsmith/cDNA_Cupcake into main

cleanup, fix for cython files

Update pyproject.toml

write_text -> open and write