Run integrated QUAST-like assembly statistics on contigs from each cell.

Run integrated QUAST-like assembly statistics on contigs from each cell.

Usage

BascetMapCellQUAST(
  bascetRoot,
  inputName = "contigs",
  outputName = "quast",
  numThreads = NULL,
  numQuastWorkers = NULL,
  minContig = 0,
  contigName = "contigs.fa",
  overwrite = FALSE,
  runner = GetDefaultBascetRunner(),
  bascetInstance = GetDefaultBascetInstance()
)

Arguments

bascetRoot

The root folder where all Bascets are stored

inputName

Name of input contig zip shard

outputName

Name of output HDF5 shard

numThreads

Total thread budget. Defaults to the runner CPU count

numQuastWorkers

Number of cells to process concurrently. If NULL, use up to 8 workers from numThreads

minContig

Minimum contig length included in primary QUAST metrics

contigName

Cell-local contig file name

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