Align from FASTQ, generate sorted and indexed BAM file

TODO Should be managed by Bascet mapshard system, with automatic input conversion. unaligned file should be made temp and removed

Usage

BascetRunCellSNP(
  bascetRoot,
  numLocalThreads = 1,
  inputName = "aligned",
  outputName = "cellsnp",
  overwrite = FALSE,
  runner = GetDefaultBascetRunner(),
  bascetInstance = GetDefaultBascetInstance()
)

Arguments

numLocalThreads

Number of threads to use for each runner

inputName

xx

outputName

xx

useReference

Name of the BWA reference to use