diff fastqc_report_render.R @ 15:d1d20f341632 draft

fastqc_report v2.0.0

--- a/fastqc_report_render.R	Wed Oct 18 22:06:39 2017 -0400
+++ b/fastqc_report_render.R	Thu Oct 19 00:11:14 2017 -0400
@@ -40,12 +40,13 @@
   ##------- 1. input data ---------------------
   args_list$ECHO = c('echo', 'e', '1', 'character')
   args_list$READS = c('reads', 'r', '1', 'character')
+  args_list$NAMES = c('names', 'n', '1', 'character')
   ##--------2. output report and outputs --------------
-  args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')
+  args_list$REPORT_HTML = c('report_html', 'o', '1', 'character')
   args_list$REPORT_DIR = c('report_dir', 'd', '1', 'character')
   args_list$SINK_MESSAGE = c('sink_message', 's', '1', 'character')
   ##--------3. .Rmd templates in the tool directory ----------
-  args_list$FASTQC_REPORT_RMD = c('fastqc_report_rmd', 't', '1', 'character')
+  args_list$FASTQC_REPORT_RMD = c('fastqc_report_rmd', 'p', '1', 'character')
   ##-----------------------------------------------------------
   opt = getopt(t(as.data.frame(args_list)))
 
@@ -68,7 +69,7 @@
       gsub('READS', opt$reads, x)
     }) %>%
     (function(x) {
-      gsub('REPORT_DIR', opt$output_dir, x)
+      gsub('REPORT_DIR', opt$report_dir, x)
     }) %>%
     (function(x) {
       fileConn = file('fastqc_report.Rmd')