.gitignore
LICENSE
MANIFEST.in
README.md
backup_pre_tidy.zip
pyproject.toml
requirements.txt
setup.py
test_samples.txt
phredator/__init__.py
phredator/__main__.py
phredator.egg-info/PKG-INFO
phredator.egg-info/SOURCES.txt
phredator.egg-info/dependency_links.txt
phredator.egg-info/entry_points.txt
phredator.egg-info/requires.txt
phredator.egg-info/top_level.txt
phredator/analyzer/__init__.py
phredator/analyzer/qc_analyzer.py
phredator/cli/__init__.py
phredator/cli/__main__.py
phredator/cli/cli.py
phredator/cli/commands.py
phredator/config/default_config.yaml
phredator/config/experiment_types/chipseq.yaml
phredator/config/experiment_types/metagenomics.yaml
phredator/config/experiment_types/rnaseq.yaml
phredator/config/experiment_types/wes.yaml
phredator/config/experiment_types/wgs.yaml
phredator/config/organisms/arabidopsis.yaml
phredator/config/organisms/cat.yaml
phredator/config/organisms/celegans.yaml
phredator/config/organisms/chicken.yaml
phredator/config/organisms/chimpanzee.yaml
phredator/config/organisms/covid19.yaml
phredator/config/organisms/cow.yaml
phredator/config/organisms/dog.yaml
phredator/config/organisms/drosophila.yaml
phredator/config/organisms/ecoli.yaml
phredator/config/organisms/frog.yaml
phredator/config/organisms/human.yaml
phredator/config/organisms/maize.yaml
phredator/config/organisms/malaria.yaml
phredator/config/organisms/monkey.yaml
phredator/config/organisms/mosquito.yaml
phredator/config/organisms/mouse.yaml
phredator/config/organisms/pig.yaml
phredator/config/organisms/rat.yaml
phredator/config/organisms/rice.yaml
phredator/config/organisms/soybean.yaml
phredator/config/organisms/tomato.yaml
phredator/config/organisms/wheat.yaml
phredator/config/organisms/yeast.yaml
phredator/config/organisms/zebrafish.yaml
phredator/fixer/__init__.py
phredator/fixer/qc_fixer.py
phredator/parser/__init__.py
phredator/parser/batch_parser.py
phredator/parser/batch_processor.py
phredator/parser/fastqc_parser.py
phredator/parser/multiqc_parser.py
phredator/pipeline/__init__.py
phredator/pipeline/pipeline_runner.py
phredator/reporter/__init__.py
phredator/reporter/report_generator.py
phredator/rules/__init__.py
phredator/rules/qc_rules.py
phredator/utils/__init__.py
phredator/utils/helpers.py
phredator/utils/profile_loader.py
phredator/utils/tool_checker.py