README.md
pyproject.toml
sunbeam/__init__.py
sunbeam/logging.py
sunbeam/bfx/__init__.py
sunbeam/bfx/decontam.py
sunbeam/bfx/parse.py
sunbeam/bfx/qc.py
sunbeam/bfx/reports.py
sunbeam/configs/apptainer_profile.yaml
sunbeam/configs/chop.yml
sunbeam/configs/default_config.yml
sunbeam/configs/default_profile.yaml
sunbeam/configs/microb120.yml
sunbeam/configs/pmacs.yml
sunbeam/configs/slurm_profile.yaml
sunbeam/extensions/.gitkeep
sunbeam/project/__init__.py
sunbeam/project/post.py
sunbeam/project/sample_list.py
sunbeam/project/sunbeam_config.py
sunbeam/project/sunbeam_profile.py
sunbeam/scripts/__init__.py
sunbeam/scripts/config.py
sunbeam/scripts/extend.py
sunbeam/scripts/init.py
sunbeam/scripts/run.py
sunbeam/scripts/sunbeam.py
sunbeam/workflow/Snakefile
sunbeam/workflow/envs/cutadapt.Dockerfile
sunbeam/workflow/envs/cutadapt.yml
sunbeam/workflow/envs/komplexity.Dockerfile
sunbeam/workflow/envs/komplexity.yml
sunbeam/workflow/envs/qc.Dockerfile
sunbeam/workflow/envs/qc.yml
sunbeam/workflow/rules/decontaminate.smk
sunbeam/workflow/rules/qc.smk
sunbeam/workflow/rules/targets.smk
sunbeam/workflow/scripts/__init__.py
sunbeam/workflow/scripts/adapter_removal_paired.py
sunbeam/workflow/scripts/adapter_removal_unpaired.py
sunbeam/workflow/scripts/aggregate_reads.py
sunbeam/workflow/scripts/fastqc_report.py
sunbeam/workflow/scripts/filter_reads.py
sunbeam/workflow/scripts/get_mapped_reads.py
sunbeam/workflow/scripts/preprocess_report.py
sunbeam/workflow/scripts/remove_low_complexity.py
sunbeam/workflow/scripts/sample_intake.py
sunbeamlib.egg-info/PKG-INFO
sunbeamlib.egg-info/SOURCES.txt
sunbeamlib.egg-info/dependency_links.txt
sunbeamlib.egg-info/entry_points.txt
sunbeamlib.egg-info/requires.txt
sunbeamlib.egg-info/top_level.txt