.gitignore
Changes.md
MANIFEST.in
README.md
baczy.png
baczy.sh
environment.yml
pyproject.toml
.github/workflows/python-publish.yaml
.github/workflows/testing.yml
baczy/__init__.py
baczy/__main__.py
baczy/baczy.CITATION
baczy/baczy.LICENSE
baczy/baczy.VERSION
baczy/setup.py
baczy.egg-info/PKG-INFO
baczy.egg-info/SOURCES.txt
baczy.egg-info/dependency_links.txt
baczy.egg-info/entry_points.txt
baczy.egg-info/requires.txt
baczy.egg-info/top_level.txt
baczy/config/config.yaml
baczy/workflow/Snakefile
baczy/workflow/envs/defensefinder.yaml
baczy/workflow/envs/phispy.yaml
baczy/workflow/rules/0.preflight.smk
baczy/workflow/rules/1.fastp.smk
baczy/workflow/rules/2.hybracter.smk
baczy/workflow/rules/2.megahit.smk
baczy/workflow/rules/3.bakta.smk
baczy/workflow/rules/4.amrfinder.smk
baczy/workflow/rules/4.phispy.smk
baczy/workflow/rules/5.defensefinder.smk
baczy/workflow/rules/6.gtdbtk.smk
baczy/workflow/rules/7.capsulefinder.smk
baczy/workflow/rules/8.summary-long.smk
baczy/workflow/rules/8.summary-short.smk
baczy/workflow/rules/9.panaroo-long.smk
baczy/workflow/rules/9.panaroo-short.smk
baczy/workflow/rules/99.targets.smk
baczy/workflow/scripts/hybractercsv.py
baczy/workflow/scripts/merge_bakta.py
sample-data/illumina/test_short_reads_low_depth_R1.fastq
sample-data/illumina/test_short_reads_low_depth_R2.fastq
sample-data/nanopore/hybracter.csv
sample-data/nanopore/test1.fastq
sample-data/nanopore/test2.fastq