diff fastq_dump_pe.Rmd @ 13:66bc1016ec2a draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty

--- a/fastq_dump_pe.Rmd	Wed Sep 27 16:49:22 2017 -0400
+++ b/fastq_dump_pe.Rmd	Wed Sep 27 16:54:07 2017 -0400
@@ -31,16 +31,11 @@
 # loop through SRA accessions to download and extract reads.
 for(id in sra_accessions) {
   if('FORMAT' == 'fasta') {
-    command = paste0('fastq-dump --fasta ', '-O read_files_directory ')
+    command = paste0('fastq-dump --fasta --split_files ', '-O read_files_directory ')
   } else {
-    command = paste0('fastq-dump ', '-O read_files_directory ')
+    command = paste0('fastq-dump --fastq --split_files ', '-O read_files_directory ')
   }
   
-  if('SPLIT_FILES' == TRUE) {
-    command = paste0(command, '--split_files ', id)
-  } else {
-    command = paste0(command, id)
-  }
   print(command)
   system(command = command)
 }