Update

Tip: It is recommended to do a fresh install in a separate directory to test a newer version.

After pulling a fresh copy of the git repository, don’t forget to update your conda environment!

mamba env update -f workflow/envs/environment.yaml

After running the newly installed version, you can compare lineage assignment changes using the following script:

python3 scripts/compare_positives.py \
  --positives-1 old_pipeline_ver/results/controls/linelists/positives.tsv \
  --positives-2 new_pipeline_ver/results/controls/linelists/positives.tsv \
  --ver-1 "old_ver" \
  --ver-2 "new_ver" \
  --outdir compare/controls \
  --node-order alphabetical

A comparative report is provided for each major or minor release: