v2.0.0

This is a major transition in progress. The version includes many things to supplement the Bactopia Nextflow pipeline, while also taking on numerous python scripts that we used through bactopia.

2.0.0

Pipeline Utility Scripts

Migrated 9 Python scripts from Nextflow module shell blocks into bactopia-py as
standalone CLI commands. These are called by the pipeline at runtime:

• bactopia-check-fastqs - verify input FASTQs meet minimum read/basepair requirements
• bactopia-check-assembly-accession - verify NCBI Assembly accessions are current and not excluded
• bactopia-cleanup-coverage - reduce redundancy in per-base coverage output
• bactopia-mask-consensus - apply coverage masking to Snippy consensus sequences
• bactopia-kraken-bracken-summary - update Bracken abundances with unclassified counts
• bactopia-scrubber-summary - create before-and-after reports from human read scrubbing
• bactopia-teton-prepare - prepare sample sheets for downstream Teton workflow analysis
• bactopia-bracken-to-excel - export Bracken abundances to Excel format

New Tools

• bactopia-lint - Bactopia-specific linter for Nextflow workflows, subworkflows, and modules
• bactopia-catalog - generate a catalog of available Bactopia workflows and modules
• bactopia-test - helper for running and reviewing nf-test results
• bactopia-review-tests - review nf-test work directories with output validation
• bactopia-prune - prune stale Nextflow work directories
• bactopia-status - show project status and recent activity

New Dependencies

• biopython - used by bactopia-check-assembly-accession and bactopia-mask-consensus
• openpyxl - used by bactopia-bracken-to-excel for Excel output

Improvements

• Migrated to ruff for formatting and linting (replaced black/flake8)
• Added test suite with pytest (182 tests covering CLI, parsers, core, and databases)
• Added GitHub Actions CI workflow for Python 3.9-3.12