From 5f1a99291e230a5d9a9f42cac8103955866cac79 Mon Sep 17 00:00:00 2001
From: Weihong Qi <weihong.qi@fgcz.ethz.ch>
Date: Fri, 12 May 2023 11:06:15 +0200
Subject: [PATCH] add html report

---
 R/app-Gce.R | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/R/app-Gce.R b/R/app-Gce.R
index bdffc809..a2b04216 100644
--- a/R/app-Gce.R
+++ b/R/app-Gce.R
@@ -18,6 +18,16 @@ ezMethodGce = function(input=NA, output=NA, param=NA, htmlFile="00index.html"){
   ezSystem(cmd)
   cmd = paste("convert", paste0(sampleName, "kmer.freq.stat_real_theory_distribution.svg"), paste0(sampleName, "kmer.freq.stat_real_theory_distribution.png"))
   ezSystem(cmd)
+
+  #html report)
+  htmlFile = output$getColumn("Report")
+  styleFiles <- file.path(system.file("templates", package="ezRun"),
+                          c("fgcz.css", "Gce.Rmd",
+                            "fgcz_header.html", "banner.png"))
+  file.copy(from=styleFiles, to=".", overwrite=TRUE)
+  params = list(sample=sampleName)
+  rmarkdown::render(input="Gce.Rmd", envir = new.env(), output_dir=".", output_file=htmlFile, quiet=TRUE)
+
   return("Success")
 }