Run Trim Galore!Source:
This function calls
system2(), and is only designed to handle standard adapter/quality
trimming. To run in parallel, register a parallel backend, e.g., using
trimgalore( filepaths, outputDir = "trimgalore_output", cmd = "trim_galore", args = NULL, pigzCmd = "pigz" )
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 ";".
Directory in which to store output. Will be created if it doesn't exist.
Name or path of the command-line interface.
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.
String for pigz command, which will gzip the output files.