AUTHORS.md
LICENSE
README.md
setup.py
src/nanogo_basecaller/__init__.py
src/nanogo_basecaller/cli.py
src/nanogo_basecaller/data_indexer.py
src/nanogo_basecaller/dorado_installer.py
src/nanogo_basecaller.egg-info/PKG-INFO
src/nanogo_basecaller.egg-info/SOURCES.txt
src/nanogo_basecaller.egg-info/dependency_links.txt
src/nanogo_basecaller.egg-info/entry_points.txt
src/nanogo_basecaller.egg-info/requires.txt
src/nanogo_basecaller.egg-info/top_level.txt
src/nanogo_basecaller/core/__init__.py
src/nanogo_basecaller/core/command.py
src/nanogo_basecaller/core/environment.py
src/nanogo_basecaller/core/parallel.py
src/nanogo_basecaller/core/resource.py
src/nanogo_basecaller/core/slurm.py
src/nanogo_basecaller/core/tool.py
src/nanogo_basecaller/tools/__init__.py
src/nanogo_basecaller/tools/basecaller/__init__.py
src/nanogo_basecaller/tools/basecaller/custom.html.j2
src/nanogo_basecaller/tools/basecaller/dorado.py
src/nanogo_basecaller/tools/basecaller/samples_sheet.py
src/nanogo_basecaller/tools/versions/__init__.py
src/nanogo_basecaller/tools/versions/env_manager.py
src/nanogo_basecaller/tools/versions/exceptions.py
src/nanogo_basecaller/tools/versions/tool_version_parser.py
src/nanogo_basecaller/tools/versions/version_checker.py
src/nanogo_basecaller/utils/__init__.py
src/nanogo_basecaller/utils/cli_select.py
src/nanogo_basecaller/utils/file_finder.py
src/nanogo_basecaller/utils/file_parser.py
src/nanogo_basecaller/utils/id_extraction.py
src/nanogo_basecaller/utils/io_selection.py
src/nanogo_basecaller/utils/path_translator.py
src/nanogo_basecaller/utils/paths.py
src/nanogo_basecaller/utils/sequencing/__init__.py
src/nanogo_basecaller/utils/sequencing/extractors.py
src/nanogo_basecaller/utils/sequencing/metadata.py
src/nanogo_basecaller/utils/sequencing/models.py
src/nanogo_basecaller/workflows/__init__.py
src/nanogo_basecaller/workflows/basecalling.py
tests/test_cli.py
tests/test_data_indexer.py