.gitignore
.gitlab-ci.yml
.pre-commit-config.yaml
AGENTS.md
CHANGELOG
Dockerfile
LICENSE
MANIFEST.in
README.md
dag.png
environment.yaml
pyproject.toml
docs/architecture.md
edentity/__init__.py
edentity/__main__.py
edentity/_version.py
edentity/cli/__init__.py
edentity/cli/args.py
edentity/cli/config.py
edentity/setup/__init__.py
edentity/setup/snakemake_setup.py
edentity/utils/__init__.py
edentity/utils/metadata_extract.py
edentity/utils/models.py
edentity/utils/snakemake_args.py
edentity/workflow/Dockerfile
edentity/workflow/Snakefile
edentity/workflow/rules/chimera.smk
edentity/workflow/rules/denoise.smk
edentity/workflow/rules/dereplication.smk
edentity/workflow/rules/filter.smk
edentity/workflow/rules/merge.smk
edentity/workflow/rules/search_exact.smk
edentity/workflow/rules/trimming.smk
edentity/workflow/scripts/chimera.py
edentity/workflow/scripts/create_multiqc_filelist.py
edentity/workflow/scripts/custom_multiqc_module.py
edentity/workflow/scripts/denoise.py
edentity/workflow/scripts/dereplication.py
edentity/workflow/scripts/esv_table.py
edentity/workflow/scripts/filter.py
edentity/workflow/scripts/merge.py
edentity/workflow/scripts/plate_summary.py
edentity/workflow/scripts/search_exact.py
edentity/workflow/scripts/trimming.py