janus

janus is a Nextflow pipeline for bacterial genome annotation using Bakta with optional functional annotation via eggNOG-mapper.

Features

• Batch annotation of bacterial genomes via a CSV samplesheet
• Per-sample configuration of genome completeness, Gram stain, and locus tag prefix
• Automatic Bakta database download when no local database is provided
• Optional eggNOG-mapper functional annotation from Bakta protein FASTA outputs
• Automatic eggNOG database download when no local database is provided

Requirements

• Nextflow >= 23.04.0
• Docker, Singularity, Apptainer, Podman, or Conda

Quick start

nextflow run exterex/janus \
    --input samplesheet.csv \
    --outdir results \
    -profile docker

Input

A CSV samplesheet with columns:

Column	Required	Description
sample	Yes	Unique sample identifier
fasta	Yes	Path to genome FASTA file
complete	No	true if genome is fully assembled (default: false)
gram	No	Gram stain: +, -, or ? (default: ?)
locus_prefix	No	Prefix for locus tags and output files (default: sample name)

Example:

sample,fasta,complete,gram,locus_prefix
ecoli_k12,genomes/ecoli.fasta,true,-,ECK
staph_aureus,genomes/s_aureus.fasta,false,+,SAU

Key parameters

Parameter	Default	Description
--input	required	Path to samplesheet CSV
--outdir	results	Output directory
--bakta_db_dir	${launchDir}/.db_cache	Directory for Bakta database (downloaded if absent)
--eggnog_run	true	Run eggNOG-mapper on Bakta protein FASTA files
--eggnog_db_dir	${launchDir}/.db_cache	Directory for eggNOG database (downloaded if absent)

Output

results/
├── bakta/
│   └── <sample>/          # Full Bakta output per sample
│       ├── <prefix>.gff3
│       ├── <prefix>.gbff
│       ├── <prefix>.fna
│       ├── <prefix>.faa
│       ├── <prefix>.ffn
│       ├── <prefix>.tsv
│       ├── <prefix>.json
│       └── <prefix>.txt
├── eggnog/
│   └── <sample>/          # eggNOG-mapper output per sample
│       └── <prefix>.emapper.*
└── pipeline_info/         # Execution reports

Profiles

Profile	Description
docker	Run with Docker containers
singularity	Run with Singularity containers
apptainer	Run with Apptainer containers
podman	Run with Podman containers
conda	Run with Conda environments
test	Minimal test dataset

Documentation

Full documentation is available at https://exterex.github.io/janus.

Citations

If you use janus in your research, please cite the tools it wraps. See CITATIONS.md.

License

MIT