# HG changeset patch
# User mingchen0919
# Date 1506562734 14400
# Node ID 2167f32cf37974632c4f3ebd6325501c8cb190db
# Parent  42e154ba2d350048576604244a51f6fcc55e2b81
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit c4beda20972367ab7d47a058a01a5f6fe492255d-dirty

diff -r 42e154ba2d35 -r 2167f32cf379 fastq_dump_pe.Rmd
--- a/fastq_dump_pe.Rmd	Wed Sep 27 21:15:56 2017 -0400
+++ b/fastq_dump_pe.Rmd	Wed Sep 27 21:38:54 2017 -0400
@@ -35,20 +35,13 @@
   } else {
     command = paste0('fastq-dump --split-files ', '-O read_files_directory ', id)
   }
+  # fastq-dump command
+  print(command)
+  # command line stdout
+  system(command = command, intern = TRUE)
 }
 ```
 
-* `fastq-dump` command
-```{r}
-print(command)
-```
-
-* `command line stdout`
-
-```{r}
-system(command = command, intern = TRUE)
-```
-
 
 # Rename files