Generate BAM with barcodes from input raw FASTQ

Generate BAM with barcodes from input raw FASTQ

Usage

BascetGetRaw(
  bascetRoot,
  rawmeta,
  outputName = "debarcoded",
  outputNameIncomplete = "incomplete_reads",
  chemistry = "atrandi_wgs",
  barcodeTolerance = NULL,
  overwrite = FALSE,
  runner = GetDefaultBascetRunner(),
  bascet_instance = GetDefaultBascetInstance()
)

Arguments

bascetRoot

The root folder where all Bascets are stored

rawmeta

Metadata for the raw FASTQ input files. See DetectRawFileMeta

outputName

Name output files: Debarcoded reads

outputNameIncomplete

Name of output files: Reads that could not be parsed

chemistry

The type of data to be parsed

barcodeTolerance

Optional: Number of mismatches allowed in the barcode for it to still be considered valid

overwrite

description

runner

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

bascet_instance

Configuration for how to run the Bascet Rust API