LICENSE
MANIFEST.in
README.md
pyproject.toml
beegees/__init__.py
beegees/__main__.py
beegees.egg-info/PKG-INFO
beegees.egg-info/SOURCES.txt
beegees.egg-info/dependency_links.txt
beegees.egg-info/entry_points.txt
beegees.egg-info/requires.txt
beegees.egg-info/top_level.txt
beegees/config/config.yaml
beegees/config/multiqc_config.yaml
beegees/config/samples_template.csv
beegees/profiles/local/config.yaml
beegees/profiles/slurm/config.yaml
beegees/resources/contaminants/human_mitogenome.fasta
beegees/resources/hmm/COI-5P.hmm
beegees/resources/hmm/rbcL.hmm
beegees/utils/__init__.py
beegees/utils/configs.py
beegees/utils/snakemake_args.py
beegees/workflow/Snakefile
beegees/workflow/scripts/01_human_cox1_filter.py
beegees/workflow/scripts/01_human_mitogenome_filter.py
beegees/workflow/scripts/02_at_content_filter.py
beegees/workflow/scripts/03_statistical_outlier_filter.py
beegees/workflow/scripts/04_reference_filter.py
beegees/workflow/scripts/05_consensus_generator.py
beegees/workflow/scripts/06_aggregate_filter_metrics.py
beegees/workflow/scripts/barcode_consensus_count.py
beegees/workflow/scripts/barcoding_outcome.py
beegees/workflow/scripts/compile_barcoding_stats.py
beegees/workflow/scripts/csv_combiner_mge.py
beegees/workflow/scripts/fastp_summary_parser.py
beegees/workflow/scripts/multiqc_plots.R
beegees/workflow/scripts/rename_headers.py
beegees/workflow/scripts/structural_validation.py
beegees/workflow/scripts/tv_blast2taxonomy.py
beegees/workflow/scripts/tv_local_blast.py
beegees/workflow/scripts/val_csv_merger.py
tests/test_aggregate_filter_metrics.py
tests/test_at_content_filter.py
tests/test_barcode_consensus_count.py
tests/test_barcoding_outcome.py
tests/test_cli.py
tests/test_compile_barcoding_stats.py
tests/test_config_validation.py
tests/test_config_yaml.py
tests/test_consensus_generator.py
tests/test_csv_combiner_mge.py
tests/test_fastp_summary_parser.py
tests/test_human_cox1_filter.py
tests/test_reference_filter.py
tests/test_snakefile_dryrun.py
tests/test_statistical_outlier_filter.py
tests/test_structural_validation.py
tests/test_tv_blast2taxonomy.py
tests/test_tv_local_blast.py
tests/test_utils.py
tests/test_val_csv_merger.py