writeHtmlReport: Write an HTML Summary Report
In ngsReports: Load FastqQC reports and other NGS related files

Description Usage Arguments Details Value Examples

Compiles an HTML report using a supplied template

writeHtmlReport(
  fastqcDir,
  template,
  outDir,
  usePlotly = TRUE,
  species = "Hsapiens",
  gcType = c("Genome", "Transcriptome"),
  nOver = 30,
  targetsDF,
  overwrite = FALSE,
  quiet = TRUE
)

`fastqcDir`	A directory containing zipped, or extracted FastQC reports
`template`	The template file which will be copied into `fastqcDir`
`outDir`	The directory to write the compiled document to
`usePlotly`	Generate interactive plots?
`species`	Species/closely related species of sequenced samples
`gcType`	Is the data "Transcriptomic" or "Genomic" in nature?
`nOver`	The maximum number of Overrepresented Sequences to show
`targetsDF`	A data.frame with at least two columns named `Filename` and `Label`. The filenames should match the original fastq files, and the labels should be simply alternative labels for these files for convenience.
`overwrite`	`logical`. Overwrite any previous copies of the template file in the destination directory
`quiet`	`logical`. Show or hide markdown output in the Console.

This will take a user supplied template, or the file supplied with the package and create an HTML summary of all standard FASTQC plots for all files in the supplied directory.

Silently returns TRUE and will output a compiled HTML file from the supplied Rmarkdown template file

## Not run: 
packageDir <- system.file("extdata", package = "ngsReports")
fileList <- list.files(packageDir, pattern = "fastqc.zip", full.names= TRUE)
# Copy these files to tempdir() to avoid overwriting
# any files in the package directory
file.copy(fileList, tempdir(), overwrite = TRUE)
writeHtmlReport(fastqcDir = tempdir())

## End(Not run)