run_fastqc: Run FastQC

In anilchalisey/parseR: Pipeline for Analysis of RNA-seq in R

Description

Run the FastQC tool

Usage

run_fastqc(fq.files = NULL, out.dir = NULL, threads = 1,
  fastqc = "fastqc")

Arguments

fq.files	Vector of the full names and paths of the fastq files.
out.dir	Path to the directory to which to write the results. If NULL, which is the default, a directory named "FASTQC" is created in the current working directory.
threads	The number of threads to use. The default is 1.
fastqc	The path to the fastqc executable. On Unix systems, if the executable is in $PATH, then it may be left as the default ("fastqc"). If it is not in $PATH, then the absolute path should be given. If using the WSL on Windows 10, then the path must be the absolute path in WSL.

Value

A directory containing the QC reports

Examples

## Not run: 
fq.files <- list.files(path = "data-raw", pattern = "*.fastq$")
fastqc(fq.files, out.dir = "FASTQ", threads = 2, fastqc = "~/bin/fastqc")

## End(Not run)

anilchalisey/parseR documentation built on May 7, 2019, 7:45 a.m.