run_fastqc: QC reports for fastq files using FastQC

In anilchalisey/chompR: ChIP and ATAC-seq data processing pipeline

Description

Run the FastQC tool to generate HTML reports. FastQC may be installed from https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Usage

run_fastqc(fastqc.files = NULL, dest.dir = "FASTQC", threads = NULL,
  fastqc = "fastqc")

Arguments

fastqc.files	character vector of paths to fastq files. [DEFAULT = NULL].
dest.dir	character string indicating directory to save results. [DEFAULT = "FASTQC"]
threads	an integer value indicating the number of parallel threads to be used by FastQC. [DEFAULT = maximum number of available threads - 1].
fastqc	a character string specifying the path to the fastqc executable. [DEFAULT = "fastqc"].

Value

character string specifying the path of the output directory.

FastQC path

If the executable is in $PATH, then the default value for paths ("fastqc") will work. If it is not in $PATH, then the absolute path should be given. If using Windows 10, it is assumed that FASTQC has been installed in WSL, and the same rules apply.

Examples

## Not run: 
fqFiles <- list.files(path = "fastqDir", pattern = "*.fastq", full.names = TRUE)
run_fastqc(fqFiles)

## End(Not run)

anilchalisey/chompR documentation built on May 9, 2019, 3:59 a.m.