Generate MultiQC report for FastQC

Source: R/run_multiqc.R

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

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())
# }