fastqscreen {seeker}

Run FastQ Screen

Description

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.

Value

A vector of exit codes, invisibly.

See Also

seeker()