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

v4.1.0 bactopia/bactopia "Cheyenne Frontier Days" 2026/08/05

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"Cheyenne Frontier Days (CFD)" ten days of rodeos, music, and carnival rides

Added

• Bactopia Tools (bactopia --wf <NAME>)
  • staphscan - Genome-based surveillance analysis of Staphylococcus aureus
  • traitar - Predict phenotypic traits from microbial genomes
• New Skills
  • /update-datasets to rebuild and publish version-pinned datasets
• Added StaphSCAN to the Staphtyper and Merlin subworkflows
• Deacon as the default host read scrubber (replaces nohuman as default)
• Deacon subworkflow orchestrating deacon/fetch and deacon/filter modules
• Three-way scrubber selection: deacon (default), nohuman (--use_nohuman), SRA Human Scrubber (--use_srascrubber)
• genomedl module and subworkflow - download assemblies from NCBI Datasets with genome-dl
  • resolves version-less accessions to the latest assembly version
  • subsamples --species downloads with --limit instead of shuf | head
  • --limit defaults to 100 to prevent downloading 50k+ genomes (--limit 0 for no limit)
  • subworkflow emits assemblies from the named fna field, and reference from gbff
• Bump internal bactopia-* pipeline tool versions
  • bactopia-gather: 1.0.5 -> 1.2.0
• bump program versions in modules
  • abritamr: 1.2.0 -> 1.3.0
  • busco: 6.0.0 -> 6.1.0
  • defense-finder: 2.0.1 -> 3.0.0
  • eggnog-mapper: 2.1.13 -> 2.1.15
  • gtdbtk: 2.7.1 -> 2.7.2
  • iqtree: 3.1.1 -> 3.1.3
  • mash: 2.3--hb105d93_10 -> 2.3--hf85e966_11
  • mlst: 2.33.1 -> 2.35.0
  • ngmaster: 2.0.0 -> 2.1.0
  • panaroo: 1.6.0 -> 1.8.0
  • phispy: 5.0.6 -> 5.0.10
  • rgi: 6.0.5 -> 6.0.8
  • staphscan: 0.3.1 -> 0.4.1

Changed

• Updated bactopia-teton meta-package from 1.1.3 to 1.1.4 (includes deacon)
• Bumped required bactopia-py to >=2.3.0 (conda meta.yaml)
• bactopia gather now downloads assemblies with genome-dl instead of ncbi-genome-download
  • --no_cache is no longer available (ncbi-genome-download specific param)
• fastani, mashtree, pangenome and snippy Bactopia Tools now download genomes with genomedl instead of ncbigenomedownload
  • --kingdom and --keep_downloads are no longer available to these tools
  • --limit now defaults to 100 for --species (previously unlimited)
  • snippy --accession requires --format genbank for an annotated reference
• Deacon modules now use bactopia-teton container instead of standalone deacon container
• Teton and scrubber workflows default to deacon instead of nohuman for host read removal
• cleanyerreads workflow supports --use_deacon flag for host read removal
• Added params.bactopia_dir (repo root) so data/ can be referenced by all workflows
• Centralized configuration for module/subworkflow tests into conf/test_base.config
• Transitioned LLM context to be provider agnostic
  • CLAUDE.md is now AGENTS.md following agents.md standard
  • .claude/docs and .claude/skills moved to .agents/docs + .agents/skills
  • Preserved Claude Code compatibility via CLAUDE.md shim and symlinks in .claude/skills
  • llms.txt and catalog.json updated with latest changes

Fixed

• float parameters being interpreted as strings in CLI
• --prokka_proteins not being found in non-Bactopia workflows
• --fastani_skip_pairwise parameter that does not exist
• mlst and amrfinderplus Bactopia Tools failing with ERROR ~ Path string cannot be empty
• mlst Bactopia Tool not falling back on bactopia/datasets
• mobsuite failing on any sample without plasmids due to compressing non-existent files
• removed unused amrfinderplus/update module
• rgi failing with unrecognized arguments: --num_threads (renamed to --threads)
• rgi_exclude_nudge replaced with rgi_include_nudge
• bactopia datasets tests requesting a version-pinned mlst.tar.gz (404)
• gubbins failing under Singularity/Apptainer when Numba tried to write to read-only container (#667) (@pvanheus)
• agrvate, gamma, and traitar modules failing under Conda with cp: '...' are the same file
• Conda errors due to loose pinnings
  • ariba, ismapper, mykrobe, shigeifinder, sistr - setuptools=80 (pkg_resources removed in setuptools 81)
  • clonalframeml (maskrc-svg) - python=3.12 (stdlib cgi removed in Python 3.13)
  • hicap - biopython=1.79 (SeqFeature.strand removed in Biopython 1.80)
  • mcroni - numpy=2.0 (reshape(newshape=) removed in NumPy 2.1)
  • clermontyping - r-readr=2.1 (quoted_na promoted to a hard error)
  • snippy (bactopia-variants) - htslib=1.14 (bcftools 1.14/htslib 1.21 ABI mismatch segfaulted bcftools consensus)
• added sample samples to ariba outputs