Run AMRfinder on contigs of all cells. This is a thin wrapper around BascetMapCell — BascetMapCellAMRfinder • Zorn

Run AMRfinder on contigs of all cells. This is a thin wrapper around BascetMapCell

Usage

BascetMapCellAMRfinder(
  bascetRoot,
  inputName = "contigs",
  outputName = "AMRfinder",
  db,
  overwrite = FALSE,
  runner = GetDefaultBascetRunner(),
  bascet_instance = GetDefaultBascetInstance()
)

Arguments

bascetRoot: The root folder where all Bascets are stored
db: description
runner: The job manager, specifying how the command will be run (e.g. locally, or via SLURM)
bascet_instance: Configuration for how to run the Bascet Rust API

Value

TODO