Parameters¶

Input/output options¶

Parameter	Default	Description
`--input`	required	Path to CSV samplesheet (sample, fasta required).
`--outdir`	`results`	Output directory for results.

Database options¶

Both databases are downloaded automatically on first run and reused on subsequent runs via Nextflow's storeDir mechanism. Point these to shared storage on HPC systems.

Parameter	Default	Description
`--bakta_db_dir`	`${launchDir}/.db_cache`	Directory where the Bakta database is stored or downloaded.
`--eggnog_db_dir`	`${launchDir}/.db_cache`	Directory where the eggNOG database is stored or downloaded.

Bakta options¶

Per-sample settings (complete, gram, locus_prefix) are set via samplesheet columns, not pipeline parameters.

Parameter	Default	Description
`--bakta_extra_args`	`""`	Additional CLI arguments passed directly to bakta.

eggNOG-mapper options¶

Parameter	Default	Description
`--eggnog_run`	`true`	Run eggNOG-mapper on Bakta protein FASTA outputs (faa).

Generic options¶

Parameter	Default	Description
`--publish_dir_mode`	`copy`	Method used to save pipeline results to output dir.
`--monochrome_logs`	`false`	Disable coloured log output.
`--help`	`false`	Display help text.
`--version`	`false`	Display version and exit.