Index a genome using BWA such that it can be used for alignment

FUTURE: could check if genome is indexed already

Usage

BascetIndexGenomeBWA(
  genomeFile,
  runner = GetDefaultBascetRunner(),
  bascetInstance = GetDefaultBascetInstance()
)

Arguments

genomeFile

Name of FASTA file holding genome sequence

runner

The job manager, specifying how the command will be run (e.g. locally, or via SLURM)

bascetInstance

A Bascet instance