diff fastq_dump_pe.Rmd @ 18:dcd0e0b6fcaf draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit e6035405141d63626702084eacd02089f816cdc7-dirty

--- a/fastq_dump_pe.Rmd	Wed Sep 27 17:12:39 2017 -0400
+++ b/fastq_dump_pe.Rmd	Wed Sep 27 20:43:32 2017 -0400
@@ -33,7 +33,7 @@
   if('FORMAT' == 'fasta') {
     command = paste0('fastq-dump --fasta --split_files ', '-O read_files_directory ')
   } else {
-    command = paste0('fastq-dump --fastq --split_files ', '-O read_files_directory ')
+    command = paste0('fastq-dump --split_files ', '-O read_files_directory ')
   }
   
   print(command)
@@ -47,6 +47,6 @@
 old_files = paste0('./read_files_directory/', list.files('./read_files_directory'))
 new_files = gsub('_1', '_forward', old_files)
 new_files = gsub('_2', '_reverse', new_files)
-file.copy('./read_files_directory/')
+file.rename(old_files, new_files)
 ```