LICENSE
MANIFEST.in
README.md
setup.py
panpiper/__init__.py
panpiper/main.py
panpiper/test.py
panpiper/workflow.py
panpiper.egg-info/PKG-INFO
panpiper.egg-info/SOURCES.txt
panpiper.egg-info/dependency_links.txt
panpiper.egg-info/entry_points.txt
panpiper.egg-info/not-zip-safe
panpiper.egg-info/requires.txt
panpiper.egg-info/top_level.txt
panpiper/tests/__init__.py
panpiper/tests/test_main.py
panpiper/tests/test_data/__init__.py
panpiper/tests/test_scripts/__init__.py
panpiper/tests/test_scripts/filter_isolates.py
panpiper/tests/test_scripts/test_concat_amrfinder.py
panpiper/workflow/assembly.smk
panpiper/workflow/pangenome.smk
panpiper/workflow/pyseer.smk
panpiper/workflow/quality.smk
panpiper/workflow/envs/amrfinder.yml
panpiper/workflow/envs/bakta.yml
panpiper/workflow/envs/bbmap.yml
panpiper/workflow/envs/bwa.yml
panpiper/workflow/envs/checkm.yml
panpiper/workflow/envs/checkm2.yml
panpiper/workflow/envs/eggnog.yml
panpiper/workflow/envs/fastani.yml
panpiper/workflow/envs/fasttree.yml
panpiper/workflow/envs/iqtree.yml
panpiper/workflow/envs/kraken.yml
panpiper/workflow/envs/mash.yml
panpiper/workflow/envs/panaroo.yml
panpiper/workflow/envs/poppunk.yml
panpiper/workflow/envs/prokka.yml
panpiper/workflow/envs/pyseer.yml
panpiper/workflow/envs/r.yml
panpiper/workflow/envs/raxml.yml
panpiper/workflow/envs/shovill.yml
panpiper/workflow/envs/unitig.yml
panpiper/workflow/envs/virsorter.yml