diff rmarkdown_samtools_flagstat_render.R @ 4:ec39bfeaf496 draft

update

--- a/rmarkdown_samtools_flagstat_render.R	Wed Dec 27 12:03:33 2017 -0500
+++ b/rmarkdown_samtools_flagstat_render.R	Wed Dec 27 15:14:47 2017 -0500
@@ -2,6 +2,7 @@
 library(rmarkdown)
 library(htmltools)
 library(dplyr)
+library(stringr)
 
 ##============ Sink warnings and errors to a file ==============
 ## use the sink() function to wrap all code within it.
@@ -58,10 +59,10 @@
       gsub('ECHO', opt$echo, x)
     }) %>%
     (function(x) {
-      gsub('REPORT_DIR', opt$output_dir, x)
+      gsub('REPORT_DIR', opt$report_dir, x)
     }) %>%
     (function(x) {
-      fileConn = file('tool_template.Rmd')
+      fileConn = file('rmarkdown_samtools_flagstat.Rmd')
       writeLines(x, con=fileConn)
       close(fileConn)
     })
@@ -70,7 +71,7 @@
   ##=============STEP 4: render .Rmd templates=================
   ##
   ##===========================================================
-  render('tool_template.Rmd', output_file = opt$report_html)
+  render('rmarkdown_samtools_flagstat.Rmd', output_file = opt$report_html)
 
 
   ##--------end of code rendering .Rmd templates----------------