Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes. mSystems. 5 (2020)

v4.0.0 bactopia/bactopia "Cream Puff" 2026/04/29

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"Cream Puff" a key component of Mash Burnedead's Muscle Magic

Changed

• Major Refactoring: Complete conversion to Nextflow 26.04 syntax and architecture
  • Minimum Nextflow version now >=26.04.0
  • Removed legacy lib/ folder in favor of nf-bactopia plugin
  • Updated all modules, subworkflows and workflows to support strict syntax requirements
  • Migrated from nextflow.preview.types to nextflow.enable.types (GA in Nextflow 26.04.0)
  • Moved all modules from modules/nf-core/ namespace to flat modules/ directory
  • Split single workflows/bactopia-tools.nf into 67 independent workflow entry points under workflows/bactopia-tools/<name>/
  • Consolidated params.config and process.config into unified module.config files
  • Adopted Nextflow record types for all module/subworkflow I/O (replaces Map-based meta)
  • Removed direct .out access in favor of result assignment
• Replaced EMPTY_* placeholder files with Path? null inputs (removed data/empty/)
• Updated output structure to use "supplemental" instead of "results" for consistency
• Improved parameter naming consistency
  • common names for similar parameters across modules and workflows
  • tool name used as a prefix to prevent overlaps in names
• Replaced meta.yml files with standardized GroovyDoc documentation in all .nf files
• Implemented type annotations in all .nf files
• Replaced publishDir with output block publishing
• Removed all when conditions in modules
• Replaced data/workflows.yml with catalog.json at repo root — a comprehensive component index covering all modules, subworkflows, and workflows with metadata
• Replaced k2scrubber with nohuman for human read removal in scrubber, cleanyerreads, and teton workflows
• Migrated pipeline utility scripts from bin/ to bactopia-py CLI commands
• Moved bactopia-prokka to modules/prokka/bin/
• Updated default max_memory from 128 GB to 144 GB and max_cpus from 4 to 12
• Reverted to pre-2025 MLST database versions due to PubMLST licensing changes

Added

• Bactopia Tools (bactopia --wf <NAME>)
  • gigatyper - Run all available MLST schemes for a species against an assembly
• New module: nohuman for human read removal
• --list_wfs to list available workflows
• --verbose flag for debug output in bactopia wrapper
• Output format validation in bactopia wrapper
• MLST now includes headers and uses sample name as label
• --emmtyper_no_header option to suppress header row in emmtyper output
• max_genome_size enforcement during assembly
• bactopia-py >=2.0.2 as a pipeline dependency
• Comprehensive documentation system (.claude/docs/)
  • Style guide and templates for GroovyDoc documentation
  • Logic rules and taxonomy for component classification
  • Technical specifications and implementation details
  • Project documentation including repository structure and development workflow
  • Reference materials with examples and troubleshooting
• Help messages to modules for improved user guidance
• Converted pytest tests to nf-test framework
• llms.txt for AI-readable project context
• Claude Code skills for AI-assisted development (.claude/skills/)
  • add-bactopia-tool - Scaffold a complete Bactopia Tool across all three tiers
  • add-module - Scaffold a new module from a bioconda/conda-forge package
  • add-subworkflow - Scaffold a new subworkflow that orchestrates existing modules
  • merge-schemas - Regenerate nextflow.config and nextflow_schema.json for workflows
  • project-status - Show a live snapshot of project state and coverage
  • review-citations - Review citation integrity across citations.yml and @citation tags
  • review-docs - Review staleness of reference docs under .claude/docs/
  • review-groovydoc - Review GroovyDoc accuracy across modules and subworkflows
  • review-tests - Review nf-test run results with diagnostic summary
  • run-tests - Run nf-tests via bactopia-test with timestamped logs
  • update-catalog - Regenerate catalog.json and llms.txt
  • update-module - Check for newer tool versions and apply updates
• Bump program versions in modules
  • abricate: 1.0.1 -> 1.4.0
  • abritamr: 1.0.19 -> 1.2.0
  • ariba: 2.14.6 -> 2.14.7
  • bakta: 1.11.0 -> 1.12.0
  • blast: 2.16.0 -> 2.17.0
  • busco: 5.8.2 -> 6.0.0
  • checkm-genome: 1.2.3 -> 1.2.5
  • checkm2: 1.0.2 -> 1.1.0
  • clonalframeml: 1.12 -> 1.13
  • defense-finder: 2.0.0 -> 2.0.1
  • ectyper: 1.0.0 -> 2.0.0
  • eggnog-mapper: 2.1.12 -> 2.1.13
  • gtdbtk: 2.4.0 -> 2.7.1
  • gubbins: 3.4 -> 3.4.3
  • iqtree: 2.4.0 -> 3.1.1
  • kleborate: 3.1.3 -> 3.2.4
  • legsta: 0.5.1 -> 0.5.2
  • lissero: 0.4.9 -> 0.4.10
  • meningotype: 0.8.5 -> 0.8.6b
  • mlst: 2.23.0 -> 2.33.1
  • ncbi-amrfinderplus: 4.0.19 -> 4.2.7
  • ngmaster: 0.5.8 -> 2.0.0
  • panaroo: 1.5.1 -> 1.6.0
  • phispy: 4.2.21 -> 5.0.6
  • prokka: 1.14.6 -> 1.15.6
  • rgi: 6.0.3 -> 6.0.5
  • seqsero2: 1.3.1 -> 1.3.2
  • snp-dists: 0.8.2 -> 1.2.0
  • sylph: 0.8.0 -> 0.9.0
  • tb-profiler: 6.6.3 -> 6.7.0
• Bump internal bactopia-* pipeline tool versions
  • bactopia-assembler: 1.0.4 -> 1.0.5
  • bactopia-gather: 1.0.4 -> 1.0.5
  • bactopia-qc: 1.0.3 -> 1.0.4
  • bactopia-sketcher: 1.0.1 -> 1.0.3
  • bactopia-teton: 1.1.1 -> 1.1.3
  • bactopia-variants: 1.0.2 -> 1.0.4

Fixed

• Corrected container build numbers for multiple modules
• AbritAMR prefix handling to use sample-specific prefixes with safe renames
• Missing configuration in Teton subworkflow
• Config path resolution issues
• Missing fastq_only parameter when using ask_merlin
• Assembler now only passes the main FASTQ type forward
• Config value using string type instead of list<string>
• Various typos throughout the codebase
• Debug information removal from production code
• Container image descriptions and fixes
• File existence checks when using file() function in Nextflow

Removed

• bin/ utility scripts (~14 Python/Bash scripts) migrated to bactopia-py CLI commands
• data/empty/ directory and all EMPTY_* placeholder files
• data/workflows.yml (replaced by catalog.json)
• Per-module meta.yml files (replaced by GroovyDoc)
• Per-module params.config and process.config files (merged into module.config)
• phyloflash module (both makedb and phyloflash submodules)
• custom/dumpsoftwareversions module (replaced by nf-bactopia plugin)
• mlst/update module due to PubMLST licensing
• custom/wget module
• workflows/updater.nf
• Single monolithic workflows/bactopia-tools.nf (replaced by per-tool workflow directories)