run_fastqc: Run FastQC

In GrahamHamilton/pipelineTools: Pipeline Tools for NGS Sequence Analysis Pipelines

Run FastQC

Description

Runs the FastQC tool, a quality control tool for high throughput sequence data

Usage

run_fastqc(
  input = NULL,
  out.dir = out.dir,
  threads = NULL,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  fastqc = NULL,
  version = FALSE
)

Arguments

input	List of all of the fastq files, forward and reverse, required
out.dir	Name of the directory to write the FastQC results, required
threads	Number of threads for FastQC
parallel	Run in parallel, default set to FALSE
cores	Number of cores/threads to use for parallel processing, default set to 4
execute	Whether to execute the commands or not, default set to TRUE
fastqc	Path to the FastQC program, required
version	Returns the version number

Value

A list with the FastQC commands

Examples

## Not run: 
fastqc.path <- "/software/FastQC-v0.11.8/fastqc"

# Version
fastqc.version <- ""
fastqc.version <- run_fastqc(fastqc = fastqc.path,
                             version = TRUE)
fastqc.version

# Run fastqc
reads.path <- "raw_reads"
mate1 <- list.files(path = reads.path, pattern = "*_R1_001.fastq.gz$", full.names = TRUE)
mate2 <- list.files(path = reads.path, pattern = "*_R2_001.fastq.gz$", full.names = TRUE)
# Merge the reads file names
all.reads <- c(mate1,mate2)

out.dir <- "fastqc"

fastqc.cmds <- run_fastqc(input = all.reads,
                          out.dir = out.dir,
                          fastqc = fastqc.path)
fastqc.cmds

## End(Not run)

GrahamHamilton/pipelineTools documentation built on Dec. 8, 2024, 3:53 p.m.