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

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

Usage

BascetMapCellAbricate(
  bascetRoot,
  inputName = "contigs",
  outputName = "abricate",
  db = "ncbi",
  args = list(),
  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

Name of ABRicate database to use (string)

args

Additional arguments passed to Bascet (list)

overwrite

Whether to overwrite existing output (logical)

runner

A runner object (e.g. LocalRunner, SlurmRunner)

bascetInstance

A Bascet instance

Value

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

See also

BascetMapCell