LICENSE
README.md
THIRD_PARTY_LICENSES.md
pyproject.toml
requirements.txt
src/metaquest/__init__.py
src/metaquest/cli.py
src/metaquest/config.py
src/metaquest/database_manager.py
src/metaquest/exceptions.py
src/metaquest/metaquest_default.yaml
src/metaquest/settings.py
src/metaquest/core/__init__.py
src/metaquest/core/analysis.py
src/metaquest/core/assembly.py
src/metaquest/core/functional_analysis.py
src/metaquest/core/preprocessing.py
src/metaquest/core/taxonomic_analysis.py
src/metaquest/io/__init__.py
src/metaquest/io/data_loaders.py
src/metaquest/io/file_validator.py
src/metaquest/io/output_formatter.py
src/metaquest/io/utils.py
src/metaquest/pipeline/__init__.py
src/metaquest/pipeline/context.py
src/metaquest/pipeline/runner.py
src/metaquest/pipeline/stages/__init__.py
src/metaquest/pipeline/stages/annotation.py
src/metaquest/pipeline/stages/assembly.py
src/metaquest/pipeline/stages/classification.py
src/metaquest/pipeline/stages/preprocessing.py
src/metaquest/pipeline/stages/reporting.py
src/metaquest/reporting/__init__.py
src/metaquest/reporting/plots.py
src/metaquest/reporting/stable_reporter.py
src/metaquest_bio.egg-info/PKG-INFO
src/metaquest_bio.egg-info/SOURCES.txt
src/metaquest_bio.egg-info/dependency_links.txt
src/metaquest_bio.egg-info/entry_points.txt
src/metaquest_bio.egg-info/requires.txt
src/metaquest_bio.egg-info/top_level.txt
tests/test_cli_interface.py
tests/test_database_and_gene_prediction.py
tests/test_fastp_reporting.py
tests/test_reporting_audit_fixes.py
tests/test_stable_boundary.py