run_multiqc: Generate MultiQC report for FastQC

In anilchalisey/rseqR: RNA-seq data processing pipeline

Description

run_multiqc generates a single HTML report from the FastQC results using MultiQC.

Usage

run_multiqc(fastqc.dir, dest.dir, multiqc = "multiqc")

Arguments

fastqc.dir	directory where all the FastQC files are saved.
dest.dir	directory to save the combined QC report.
multiqc	a character string specifying the path to the multiqc executable. [DEFAULT = "multiqc"].

Value

HTML report.

MultiQC path

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

References

Philip Ewels, Mans Magnusson, Sverker Lundin, and Max Kaller (2016): MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047-3048. https://doi.org/10.1093/bioinformatics/btw354

Examples

## Not run: 
run_multiqc(fastqc.dir=tempdir(), dest.dir=tempdir())

## End(Not run)

anilchalisey/rseqR documentation built on May 25, 2019, 2:25 p.m.