LICENSE
README.md
pyproject.toml
nose_pipeline/__init__.py
nose_pipeline/cli.py
nose_pipeline.egg-info/PKG-INFO
nose_pipeline.egg-info/SOURCES.txt
nose_pipeline.egg-info/dependency_links.txt
nose_pipeline.egg-info/entry_points.txt
nose_pipeline.egg-info/requires.txt
nose_pipeline.egg-info/top_level.txt
nose_pipeline/pipeline_files/QUICK_START.md
nose_pipeline/pipeline_files/README.md
nose_pipeline/pipeline_files/Run-pipeline.py
nose_pipeline/pipeline_files/WORKFLOW.md
nose_pipeline/pipeline_files/config_sync.py
nose_pipeline/pipeline_files/report_common.py
nose_pipeline/pipeline_files/requirements.txt
nose_pipeline/pipeline_files/Module1/Eukaryotic_genome_summary.py
nose_pipeline/pipeline_files/Module1/Module1.sh
nose_pipeline/pipeline_files/Module1/Nose_Module1.sh
nose_pipeline/pipeline_files/Module1/Prokaryotic_genome_summary.py
nose_pipeline/pipeline_files/Module1/README.md
nose_pipeline/pipeline_files/Module1/generate_report.py
nose_pipeline/pipeline_files/Module1/snakefile
nose_pipeline/pipeline_files/Module1/envs/cat.yaml
nose_pipeline/pipeline_files/Module1/envs/checkm2.yaml
nose_pipeline/pipeline_files/Module1/envs/eukcc.yaml
nose_pipeline/pipeline_files/Module1/envs/gtdbtk.yaml
nose_pipeline/pipeline_files/Module1/envs/quast.yaml
nose_pipeline/pipeline_files/Module2/Module2.sh
nose_pipeline/pipeline_files/Module2/Nose_Module2.sh
nose_pipeline/pipeline_files/Module2/README.md
nose_pipeline/pipeline_files/Module2/aai.rb
nose_pipeline/pipeline_files/Module2/auto_hmm_outgroup.py
nose_pipeline/pipeline_files/Module2/compile_results_16S.py
nose_pipeline/pipeline_files/Module2/compile_results_WGS.py
nose_pipeline/pipeline_files/Module2/download_genomes.sh
nose_pipeline/pipeline_files/Module2/generate_report.py
nose_pipeline/pipeline_files/Module2/lpsn.csv
nose_pipeline/pipeline_files/Module2/ncbi_readme.md
nose_pipeline/pipeline_files/Module2/pocp.sh
nose_pipeline/pipeline_files/Module2/prepare_tree_inputs.py
nose_pipeline/pipeline_files/Module2/snakefile_16S
nose_pipeline/pipeline_files/Module2/snakefile_WGS
nose_pipeline/pipeline_files/Module2/snakefile_filtering
nose_pipeline/pipeline_files/Module2/envs/aai.yaml
nose_pipeline/pipeline_files/Module2/envs/barrnap.yaml
nose_pipeline/pipeline_files/Module2/envs/blast.yaml
nose_pipeline/pipeline_files/Module2/envs/fastani.yaml
nose_pipeline/pipeline_files/Module2/envs/ncbi.yaml
nose_pipeline/pipeline_files/Module2/envs/prokka.yaml
nose_pipeline/pipeline_files/Module3/Module3.sh
nose_pipeline/pipeline_files/Module3/Nose_Module3.sh
nose_pipeline/pipeline_files/Module3/README.md
nose_pipeline/pipeline_files/Module3/generate_report.py
nose_pipeline/pipeline_files/Module3/gtotree_snakefile
nose_pipeline/pipeline_files/Module3/iqtree_snakefile
nose_pipeline/pipeline_files/Module3/pre_gtotree_snakefile
nose_pipeline/pipeline_files/Module3/tree_annotation.py
nose_pipeline/pipeline_files/Module3/envs/gtotree.yaml
nose_pipeline/pipeline_files/Module3/envs/iqtree.yaml
nose_pipeline/pipeline_files/Module3/envs/ncbi_datasets.yaml
nose_pipeline/pipeline_files/Module4/Module4.sh
nose_pipeline/pipeline_files/Module4/Nose_Module4.sh
nose_pipeline/pipeline_files/Module4/README.md
nose_pipeline/pipeline_files/Module4/merge_results.py
nose_pipeline/pipeline_files/Module4/snakefile
nose_pipeline/pipeline_files/Module4/envs/sylph.yaml
nose_pipeline/pipeline_files/Module5/Module5.sh
nose_pipeline/pipeline_files/Module5/Nose_Module5.sh
nose_pipeline/pipeline_files/Module5/README.md
nose_pipeline/pipeline_files/Module5/cog_merge.py
nose_pipeline/pipeline_files/Module5/compile_functional_summary.py
nose_pipeline/pipeline_files/Module5/generate_report.py
nose_pipeline/pipeline_files/Module5/genomad_merge.py
nose_pipeline/pipeline_files/Module5/parserfile.py
nose_pipeline/pipeline_files/Module5/snakefile
nose_pipeline/pipeline_files/Module5/envs/abricate.yaml
nose_pipeline/pipeline_files/Module5/envs/antismash.yaml
nose_pipeline/pipeline_files/Module5/envs/cogclassifier.yaml
nose_pipeline/pipeline_files/Module5/envs/genomad.yaml
nose_pipeline/pipeline_files/Module5/envs/prokka.yaml
nose_pipeline/pipeline_files/Module6/Module6.sh
nose_pipeline/pipeline_files/Module6/Nose_Module6.sh
nose_pipeline/pipeline_files/Module6/README.md
nose_pipeline/pipeline_files/Module6/compile_model_summary.py
nose_pipeline/pipeline_files/Module6/generate_model_stats.py
nose_pipeline/pipeline_files/Module6/generate_report.py
nose_pipeline/pipeline_files/Module6/snakefile
nose_pipeline/pipeline_files/Module6/envs/carveme.yaml
nose_pipeline/pipeline_files/Module6/envs/memote.yaml
nose_pipeline/pipeline_files/Module6/envs/py39.yaml
nose_pipeline/pipeline_files/scripts/download_databases.sh
nose_pipeline/pipeline_files/scripts/setup_wsl.sh
nose_pipeline/pipeline_files/templates/dashboard.html
tests/test_cli_wsl_routing.py
tests/test_line_endings.py