Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump

diff fastq_dump_se.Rmd @ 6:4c84d748da08 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit c9517f0b061cdca3b79678d9a2620e1e43115d42-dirty
author mingchen0919
date Wed, 27 Sep 2017 11:40:38 -0400
parents 7ec600e7dba7
children 233210d44681
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line diff
--- a/fastq_dump_se.Rmd	Wed Sep 27 11:18:27 2017 -0400
+++ b/fastq_dump_se.Rmd	Wed Sep 27 11:40:38 2017 -0400
@@ -31,11 +31,12 @@
 # loop through SRA accessions to download and extract reads.
 for(id in sra_accessions) {
   if(FORMAT == 'fasta') {
-    command = paste0('fastq-dump --fasta ', id, ' -O read_files_directory')
+    command = paste0('fastq-dump --fasta ', '-O read_files_directory ', id)
   } else {
-    command = paste0('fastq-dump ', id, ' -O read_files_directory')
+    command = paste0('fastq-dump ', '-O read_files_directory ', id)
   }
-  system(command = command)
+  print(command)
+  #system(command = command)
 }
 ```