run_fastqc: Run FastQC

Description Usage Arguments Value Examples

View source: R/run_fastqc.R

Description

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

Usage

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run_fastqc(
  reads = reads,
  out.dir = out.dir,
  threads = NULL,
  fastqc = NULL,
  version = FALSE
)

Arguments

reads

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

fastqc

Path to the FastQC program, required

version

Returns the version number

Value

A list with the FastQC commands

Examples

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## 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(reads = all.reads,
                          out.dir = out.dir,
                          fastqc = fastqc.path)
fastqc.cmds

## End(Not run)

GrahamHamilton/pipelineTools documentation built on June 19, 2021, 1:08 p.m.