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/launch_ui.py
nose_pipeline/pipeline_files/nose_config.yaml
nose_pipeline/pipeline_files/requirements.txt
nose_pipeline/pipeline_files/run.sh
nose_pipeline/pipeline_files/run_M2_to_M6.sh
nose_pipeline/pipeline_files/run_ui.bat
nose_pipeline/pipeline_files/Input files/README.md
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/config.yaml
nose_pipeline/pipeline_files/Module1/snakefile
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/config.yaml
nose_pipeline/pipeline_files/Module2/config.yaml.windows_backup
nose_pipeline/pipeline_files/Module2/download_genomes.sh
nose_pipeline/pipeline_files/Module2/filtering_complete.marker
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/Module3/Module3.sh
nose_pipeline/pipeline_files/Module3/Nose_Module3.sh
nose_pipeline/pipeline_files/Module3/README.md
nose_pipeline/pipeline_files/Module3/config.yaml
nose_pipeline/pipeline_files/Module3/genome_summary_for_tree.csv
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/Module4/Module4.sh
nose_pipeline/pipeline_files/Module4/Nose_Module4.sh
nose_pipeline/pipeline_files/Module4/README.md
nose_pipeline/pipeline_files/Module4/config.yaml
nose_pipeline/pipeline_files/Module4/merge_results.py
nose_pipeline/pipeline_files/Module4/snakefile
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/config.yaml
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/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/config.yaml
nose_pipeline/pipeline_files/Module6/generate_model_stats.py
nose_pipeline/pipeline_files/Module6/snakefile
nose_pipeline/pipeline_files/scripts/download_databases.sh
nose_pipeline/pipeline_files/scripts/setup_wsl.sh
nose_pipeline/pipeline_files/templates/dashboard.html
nose_pipeline/pipeline_files/templates/index.html