Produce a count matrix of taxonomy IDs from KRAKEN output

Usage

BascetMakeKrakenCountMatrix(
  bascetRoot,
  numLocalThreads = NULL,
  inputName = "kraken_out",
  outputName = "kraken",
  overwrite = FALSE,
  runner = GetDefaultBascetRunner(),
  bascetInstance = GetDefaultBascetInstance()
)

Arguments

bascetRoot: The root folder where all Bascets are stored
numLocalThreads: Number of threads for KRAKEN to use. Default is the maximum, taken from runner settings
inputName: Name of input shard (KRAKEN output)
outputName: Name of output shard (h5 count matrix)
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