R/summary.R

In FASTGenomics/fastgenomicsR: Facilitates the use of the FASTGenomics backend.

#' Write an markdown summary using knitr
#' 
#' Knitr will use the global environment, so your top level objects should be 
#' acessible.
#' the result is written to outputdirectory/summary/summary.md
#' 
#' @param fg_process the current FASTGenomics Process.
#' @param summary_path the path to the summary to be knitted.
#'
#' @export
#' 
#' @return NA
#' 
#' @examples
#' fg_process <- Process()
#' everything <- 42
#' write_summary(fg_processs, everything)
write_summary <- function(process, summary_path=""){
  
  if (summary_path == "") {
    summary_path <- file.path(process@app@dir, "summary.md")
  }
  
  assertthat::is.readable(summary_path)
  
  knitr::knit(summary_path, process@output[[SUMMARY_KEY]]@path, envir = globalenv())
}