Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump

changeset 20:2167f32cf379 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit c4beda20972367ab7d47a058a01a5f6fe492255d-dirty
author mingchen0919
date Wed, 27 Sep 2017 21:38:54 -0400
parents 42e154ba2d35
children 3c859d094074
files fastq_dump_pe.Rmd
diffstat 1 files changed, 4 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- 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