python-scripts/bactopia-atb-downloader
python-scripts/bactopia-atb-formatter
python-scripts/bactopia-bracken-to-excel
python-scripts/bactopia-catalog
python-scripts/bactopia-check-assembly-accession
python-scripts/bactopia-check-fastqs
python-scripts/bactopia-citations
python-scripts/bactopia-cleanup-coverage
python-scripts/bactopia-datasets
python-scripts/bactopia-docs
python-scripts/bactopia-download
python-scripts/bactopia-kraken-bracken-summary
python-scripts/bactopia-lint
python-scripts/bactopia-mask-consensus
python-scripts/bactopia-merge-schemas
python-scripts/bactopia-prepare
python-scripts/bactopia-prune
python-scripts/bactopia-pubmlst-build
python-scripts/bactopia-pubmlst-setup
python-scripts/bactopia-review-tests
python-scripts/bactopia-scaffold
python-scripts/bactopia-scrubber-summary
python-scripts/bactopia-search
python-scripts/bactopia-status
python-scripts/bactopia-summary
python-scripts/bactopia-sysinfo
python-scripts/bactopia-test
python-scripts/bactopia-teton-prepare
python-scripts/bactopia-update
python-scripts/bactopia-workflows
site-packages/bactopia-2.1.2.dist-info/INSTALLER
site-packages/bactopia-2.1.2.dist-info/METADATA
site-packages/bactopia-2.1.2.dist-info/RECORD
site-packages/bactopia-2.1.2.dist-info/REQUESTED
site-packages/bactopia-2.1.2.dist-info/WHEEL
site-packages/bactopia-2.1.2.dist-info/direct_url.json
site-packages/bactopia-2.1.2.dist-info/entry_points.txt
site-packages/bactopia-2.1.2.dist-info/licenses/LICENSE
site-packages/bactopia/__init__.py
site-packages/bactopia/atb.py
site-packages/bactopia/cli/__init__.py
site-packages/bactopia/cli/atb/__init__.py
site-packages/bactopia/cli/atb/atb_downloader.py
site-packages/bactopia/cli/atb/atb_formatter.py
site-packages/bactopia/cli/catalog.py
site-packages/bactopia/cli/citations.py
site-packages/bactopia/cli/datasets.py
site-packages/bactopia/cli/docs.py
site-packages/bactopia/cli/download.py
site-packages/bactopia/cli/helpers/__init__.py
site-packages/bactopia/cli/helpers/merge_schemas.py
site-packages/bactopia/cli/jsonify.py
site-packages/bactopia/cli/lint.py
site-packages/bactopia/cli/pipeline/__init__.py
site-packages/bactopia/cli/pipeline/bracken_to_excel.py
site-packages/bactopia/cli/pipeline/check_assembly_accession.py
site-packages/bactopia/cli/pipeline/check_fastqs.py
site-packages/bactopia/cli/pipeline/cleanup_coverage.py
site-packages/bactopia/cli/pipeline/kraken_bracken_summary.py
site-packages/bactopia/cli/pipeline/mask_consensus.py
site-packages/bactopia/cli/pipeline/scrubber_summary.py
site-packages/bactopia/cli/pipeline/teton_prepare.py
site-packages/bactopia/cli/prepare.py
site-packages/bactopia/cli/prune.py
site-packages/bactopia/cli/pubmlst/build.py
site-packages/bactopia/cli/pubmlst/setup.py
site-packages/bactopia/cli/review.py
site-packages/bactopia/cli/scaffold.py
site-packages/bactopia/cli/search.py
site-packages/bactopia/cli/status.py
site-packages/bactopia/cli/summary.py
site-packages/bactopia/cli/sysinfo.py
site-packages/bactopia/cli/testing.py
site-packages/bactopia/cli/update.py
site-packages/bactopia/cli/workflows.py
site-packages/bactopia/conda.py
site-packages/bactopia/databases/__init__.py
site-packages/bactopia/databases/ena.py
site-packages/bactopia/databases/ncbi.py
site-packages/bactopia/databases/pubmlst/__init__.py
site-packages/bactopia/databases/pubmlst/constants.py
site-packages/bactopia/databases/pubmlst/utils.py
site-packages/bactopia/lint/__init__.py
site-packages/bactopia/lint/citations.py
site-packages/bactopia/lint/docs.py
site-packages/bactopia/lint/models.py
site-packages/bactopia/lint/rules/__init__.py
site-packages/bactopia/lint/rules/module_rules.py
site-packages/bactopia/lint/rules/subworkflow_rules.py
site-packages/bactopia/lint/rules/workflow_rules.py
site-packages/bactopia/lint/runner.py
site-packages/bactopia/nf.py
site-packages/bactopia/outputs.py
site-packages/bactopia/parse.py
site-packages/bactopia/parsers/__init__.py
site-packages/bactopia/parsers/amrfinderplus.py
site-packages/bactopia/parsers/annotator.py
site-packages/bactopia/parsers/ariba.py
site-packages/bactopia/parsers/assembler.py
site-packages/bactopia/parsers/blast.py
site-packages/bactopia/parsers/citations.py
site-packages/bactopia/parsers/coverage.py
site-packages/bactopia/parsers/error.py
site-packages/bactopia/parsers/gather.py
site-packages/bactopia/parsers/generic.py
site-packages/bactopia/parsers/kraken.py
site-packages/bactopia/parsers/mapping.py
site-packages/bactopia/parsers/mlst.py
site-packages/bactopia/parsers/nextflow.py
site-packages/bactopia/parsers/parsables.py
site-packages/bactopia/parsers/qc.py
site-packages/bactopia/parsers/sketcher.py
site-packages/bactopia/parsers/variants.py
site-packages/bactopia/parsers/versions.py
site-packages/bactopia/parsers/workflows.py
site-packages/bactopia/reports/__init__.py
site-packages/bactopia/reports/templates/__init__.py
site-packages/bactopia/scaffold.py
site-packages/bactopia/summary.py
site-packages/bactopia/templates/__init__.py
site-packages/bactopia/templates/bactopia/llms.txt.j2
site-packages/bactopia/templates/logos.py
site-packages/bactopia/templates/nextflow/nextflow.config.j2
site-packages/bactopia/templates/nextflow/params.config.j2
site-packages/bactopia/templates/nextflow/process.config.j2
site-packages/bactopia/templates/scaffold/module/main.nf.j2
site-packages/bactopia/templates/scaffold/module/module.config.j2
site-packages/bactopia/templates/scaffold/module/schema.json.j2
site-packages/bactopia/templates/scaffold/module/tests/main.nf.test.j2
site-packages/bactopia/templates/scaffold/module/tests/nextflow.config.j2
site-packages/bactopia/templates/scaffold/module/tests/nf-test.config.j2
site-packages/bactopia/templates/scaffold/subworkflow/main.nf.j2
site-packages/bactopia/templates/scaffold/subworkflow/tests/main.nf.test.j2
site-packages/bactopia/templates/scaffold/subworkflow/tests/nextflow.config.j2
site-packages/bactopia/templates/scaffold/subworkflow/tests/nf-test.config.j2
site-packages/bactopia/templates/scaffold/subworkflow/tests/nftignore.j2
site-packages/bactopia/templates/scaffold/workflow/main.nf.j2
site-packages/bactopia/templates/scaffold/workflow/nextflow.config.j2
site-packages/bactopia/templates/scaffold/workflow/tests/main.nf.test.j2
site-packages/bactopia/templates/scaffold/workflow/tests/nf-test.config.j2
site-packages/bactopia/templates/scaffold/workflow/tests/nftignore.j2
site-packages/bactopia/utils.py
