# HG changeset patch
# User mingchen0919
# Date 1506546398 14400
# Node ID 883f102eb22792125affdc88c86139d9cefb8745
# Parent  627c487d22e32eea4741a6441d7fd2f52878c430
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty

diff -r 627c487d22e3 -r 883f102eb227 fastq_dump_pe_render.R
--- a/fastq_dump_pe_render.R	Wed Sep 27 17:05:22 2017 -0400
+++ b/fastq_dump_pe_render.R	Wed Sep 27 17:06:38 2017 -0400
@@ -54,7 +54,8 @@
 library(dplyr)
 
 #----- 1. create the report directory ------------------------
-system(paste0('mkdir -p ', opt$output_dir))
+# system(paste0('mkdir -p ', opt$output_dir))
+dir.create(opt$output_dir)
 
 #----- 2. generate Rmd files with Rmd templates --------------
 #   a. templates without placeholder variables: