bactopia-tests

Test datasets for Bactopia, a Nextflow pipeline for the complete analysis of bacterial genomes. This repository provides sequencing reads, assemblies, reference databases, and pre-computed results used by Bactopia's CI/CD tests.

Testing Quick Start

Here's a quick setup for using bactopia-tests with the latest tests from bactopia. This might be out of sync with latest bactopia builds, so please refer to them for the latest instructions.

mkdir ~/bactopia-repos
cd ~/bactopia-repos
git clone https://github.com/bactopia/bactopia.git
git clone https://github.com/bactopia/bactopia-py.git
git clone https://github.com/bactopia/bactopia-tests.git
git clone https://github.com/bactopia/nf-bactopia.git

# Create and activate a conda environment for bactopia-dev
cd bactopia
conda create -y -n bactopia-pev -f environment.yml
conda activate bactopia-pev

# Install latest bactopia-py from source
cd ../bactopia-py
just install

# Install nf-bactopia plugin
cd ../nf-bactopia
make assemble
make install

# Run tests using the test datasets
cd ../bactopia
# test modules
bactopia-test \
    --bactopia-path ~/bactopia-repos/bactopia \
    --test-data ~/bactopia-repos/bactopia-tests \
    --tier modules \
    --jobs 4

# test subworkflows
bactopia-test \
    --bactopia-path ~/bactopia-repos/bactopia \
    --test-data ~/bactopia-repos/bactopia-tests \
    --tier subworkflows \
    --jobs 4

# test workflows
bactopia-test \
    --bactopia-path ~/bactopia-repos/bactopia \
    --test-data ~/bactopia-repos/bactopia-tests \
    --tier workflows \
    --jobs 4

# test everything
bactopia-test \
    --bactopia-path ~/bactopia-repos/bactopia \
    --test-data ~/bactopia-repos/bactopia-tests \
    --tier all \
    --jobs 4

Directory Structure

bactopia-tests/
├── species/      # Test data organized by bacterial species
├── datasets/     # Tool-specific reference databases and results
└── empty/        # Empty placeholder files for error handling tests

Species

Species	Accession(s)	Genome Size	Data Types
Bacillus anthracis	GCF_000008445	-	Assembly
Escherichia coli	GCF_001695515	5.87 Mb	Assembly
Escherichia coli (mcr-1)	GCF_001682305	4.62 Mb	Assembly
Glaesserella parasuis	GCF_002777395	2.48 Mb	Assembly
Haemophilus influenzae	GCA_000027305, GCF_900478275	1.89 Mb	Assembly, Annotation
Klebsiella pneumoniae	GCF_000009885	5.47 Mb	Assembly
Legionella pneumophila	GCF_000048645	3.64 Mb	Assembly
Listeria monocytogenes	GCF_002285835	3.15 Mb	Assembly
Mixed	Multiple	-	Illumina reads, Annotations
Neisseria gonorrhoeae	GCF_001047255	2.17 Mb	Assembly
Neisseria meningitidis	GCF_003355215	2.31 Mb	Assembly
Portiera	SRR2838702, ERR3772599	358 kb	Illumina, Nanopore, Assembly, Annotation, Sketches
Pseudomonas aeruginosa	GCF_000006765	6.26 Mb	Assembly
Salmonella enterica	GCF_016028495	4.97 Mb	Assembly
Shigella boydii	GCF_016726285	4.55 Mb	Assembly
Shigella dysenteriae	GCF_002949675, ERR6005894, SRR13039589	4.58 Mb	Assembly, Illumina, Nanopore
Staphylococcus aureus	GCF_000017085	2.90 Mb	Assembly
Streptococcus pneumoniae	GCF_001457635, ERR1438863	2.11 Mb	Assembly, Illumina
Streptococcus pyogenes	GCF_006364235	1.91 Mb	Assembly
Streptococcus suis	GCF_002285535	2.07 Mb	Assembly

Datasets

Databases

Dataset	Description
amrfinderplus	AMRFinderPlus antimicrobial resistance gene database
ariba	ARIBA pre-processed CARD and VFDB databases
defensefinder	DefenseFinder bacterial defense system models
emmtyper	EMM type reference sequences for S. pyogenes
ismapper	IS element reference sequences
mlst	Multi-locus sequence typing allele and profile database
variants	RefSeq genome Mash sketches

Test Sequences

Dataset	Description
blast	Gene, primer, and protein sequences for BLAST searches
generic	Reference genomes, GFFs, metadata, and pan-genome data
mapping-sequences	Short reference sequences for read mapping

Pre-computed Results

Dataset	Description
bracken	Bracken taxonomic classification output
genotyphi	GenoTyphi Salmonella Typhi genotyping output
rgi	RGI/CARD resistance gene identifier output
snippy	Snippy variant calling output (VCF and aligned FASTA)
tbprofiler	TBProfiler results for Illumina and Nanopore

Symlinked Databases

The following datasets are symlinks to large external database caches and are not tracked in this repository: bakta, checkm2, eggnog, gtdbtk, kraken2, midas, nohuman, sketcher, srahumanscrubber, sylph.

Empty Files

The empty/ directory contains 21 empty files (e.g., EMPTY_R1.fastq.gz, EMPTY_ASSEMBLY) used to verify that Bactopia handles missing or empty input gracefully.

Machine-Readable Files

• llms.txt -- LLM-friendly project overview (llmstxt.org format)
• catalog.json -- Structured metadata for all species, datasets, and files

License

MIT