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

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(),
  bascetInstance = GetDefaultBascetInstance()
)

Arguments

bascetRoot

The root folder where all Bascets are stored

inputName

Name of input shard

outputName

Name of output shard

db

Path to database

overwrite

Force overwriting of existing files. The default is to do nothing files exist

runner

The job manager, specifying how the command will be run (e.g. locally, or via SLURM)

bascetInstance

A Bascet instance

Value

A job to be executed, or being executed, depending on runner settings