Run Trim Galore! — trimgalore • seeker

This function calls trim_galore using system2(), and is only designed to handle standard adapter/quality trimming. To run in parallel, register a parallel backend using doFuture::registerDoFuture() or doParallel::registerDoParallel().

trimgalore(
  filepaths,
  outputDir = "trimgalore_output",
  cmd = "trim_galore",
  args = NULL
)

Arguments

filepaths	Paths to fastq files. For single-end reads, each element should be a single filepath. For paired-end reads, each element should be two filepaths separated by ";".
outputDir	Directory in which to store output. Will be created if it doesn't exist.
cmd	Name or path of the command-line interface.
args	Additional arguments to pass to the command-line interface. Output files will always be compressed. Arguments "dont_gzip", "--cores", "-j", and "--basename" are not allowed. Arguments "-o" and "--paired" should not be specified here.

A vector of exit codes, invisibly.