This function calls
fastq_screen
using system2(). To run in parallel, register a parallel backend, e.g.,
using doParallel::registerDoParallel().
Usage
fastqscreen(
filepaths,
outputDir = "fastqscreen_output",
cmd = "fastq_screen",
args = c("--threads", foreach::getDoParWorkers(), "--conf",
"~/FastQ_Screen_Genomes/fastq_screen.conf")
)Arguments
- filepaths
Paths to fastq files. For single-end reads, each element should be a single filepath. For paired-end reads, each element can 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.