Usage

Samplesheet

The pipeline requires a CSV samplesheet. Only sample and fasta are required.

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_k12.fasta,true,-,ECK
staph_aureus,genomes/s_aureus.fasta,false,+,SAU
b_subtilis,genomes/b_subtilis.fasta,,,BSU

Empty fields are treated as "not provided" and fall back to defaults.

Basic usage

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

Specifying database locations

Both databases are downloaded automatically on first run and cached for subsequent runs. Use --bakta_db_dir and --eggnog_db_dir to control where they are stored — useful for shared HPC storage where the same databases are reused across users and projects.

nextflow run exterex/janus \
    --input samplesheet.csv \
    --bakta_db_dir /shared/databases/bakta \
    --eggnog_db_dir /shared/databases/eggnog \
    --outdir results \
    -profile docker

Disabling eggNOG-mapper

eggNOG-mapper runs by default. To skip it:

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

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

Resuming a run

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