Align from FASTQ, generate sorted and indexed BAM file

Usage

BascetAlignToReference(
  bascetRoot,
  useReference,
  numThreads = NULL,
  totalMem = NULL,
  inputName = "filtered",
  outputName = "aligned",
  outputNameBAMcell = NULL,
  outputNameBAMpos = NULL,
  overwrite = FALSE,
  aligner = c(NULL, "BWAMEM2", "STAR", "minimap2"),
  bwamem2BatchPairs = NULL,
  runner = GetDefaultBascetRunner(),
  bascetInstance = GetDefaultBascetInstance()
)

Arguments

bascetRoot: The root folder where all Bascets are stored
useReference: Name of the BWA reference to use
numThreads: Number of threads to use for each runner. Default is the maximum, taken from runner settings
totalMem: Total memory to allocate
inputName: Name of input shard
outputName: Output shard name prefix. Defaults to <outputName>_cell for the unsorted/cell BAM and <outputName>_pos for the position-sorted BAM.
outputNameBAMcell: Name of cell-sorted BAMs. If NULL, derived from outputName.
outputNameBAMpos: Name of pos-sorted BAMs. If NULL, derived from outputName.
overwrite: Force overwriting of existing files. The default is to do nothing files exist
aligner: Which aligner to use: "BWAMEM2", "STAR", or "minimap2"
bwamem2BatchPairs: For aligner "BWAMEM2" only: max read pairs per alignment batch. Bounds per-batch peak memory (bwa-mem2 materialises a whole batch's alignment scratch + SAM before returning). If NULL (default), bascet uses its built-in default (100000). Lower it on memory-constrained nodes, raise it for throughput.
runner: The job manager, specifying how the command will be run (e.g. locally, or via SLURM)
bascetInstance: A Bascet instance