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, e.g., using
doParallel::registerDoParallel().
Usage
trimgalore(
filepaths,
outputDir = "trimgalore_output",
cmd = "trim_galore",
args = NULL,
pigzCmd = "pigz"
)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 "--gzip", "--cores", "-j", and "--basename" are not allowed. Arguments "-o" and "--paired" should not be specified here.
- pigzCmd
String for pigz command, which will gzip the output files.