Run KRAKEN2 for each cell. Then produce a count matrix of taxonomy IDs from the output

Run KRAKEN2 for each cell. Then produce a count matrix of taxonomy IDs from the output

Usage

BascetRunKraken(
  bascetRoot,
  useKrakenDB = NULL,
  numThreads = NULL,
  inputName = "filtered",
  outputRawName = "kraken_raw",
  outputMatrixName = "kraken_mat",
  overwrite = FALSE,
  runner = GetDefaultBascetRunner(),
  bascetInstance = GetDefaultBascetInstance()
)

Arguments

bascetRoot

The root folder where all Bascets are stored

useKrakenDB

Path to KRAKEN2 database

numThreads

Number of threads for one KRAKEN instance

inputName

Name of input shard (FASTQ)

outputRawName

Name of output shard (kraken raw output)

outputMatrixName

Name of output shard (kraken count table data)

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