Produce a count matrix of taxonomy IDs from KRAKEN output — BascetMakeKrakenCountMatrix • Zorn

TODO: should run kraken in the same run

Usage

BascetMakeKrakenCountMatrix(
  bascetRoot,
  numLocalThreads = 1,
  inputName = "kraken_out",
  outputName = "kraken",
  overwrite = FALSE,
  runner = GetDefaultBascetRunner(),
  bascet_instance = GetDefaultBascetInstance()
)

Arguments

bascetRoot: The root folder where all Bascets are stored
numLocalThreads: description
inputName: description
outputName: 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
useKrakenDB: description