fastqc: Run FastQC
In seeker: Simplified Fetching and Processing of Microarray and RNA-Seq Data

fastqc

R Documentation

Run FastQC

This function calls fastqc using system2(). To run in parallel, register a parallel backend, e.g., using doParallel::registerDoParallel().

fastqc(filepaths, outputDir = "fastqc_output", cmd = "fastqc", args = NULL)

`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.

A vector of exit codes, invisibly.