Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump

diff fastq_dump_pe.Rmd @ 3:b70047273f38 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit b212086a85c4d1e62e0d0c0e77b6f3fcabea04ef-dirty
author mingchen0919
date Mon, 16 Oct 2017 17:21:26 -0400
parents 58d48d1157ed
children
line wrap: on
line diff
--- a/fastq_dump_pe.Rmd	Mon Oct 16 16:53:21 2017 -0400
+++ b/fastq_dump_pe.Rmd	Mon Oct 16 17:21:26 2017 -0400
@@ -30,7 +30,7 @@
 sra_accessions = sra_accessions[sra_accessions != '']
 # loop through SRA accessions to download and extract reads.
 for(id in sra_accessions) {
-  if('FORMAT' == 'No') {
+  if('FORMAT' == 'fasta') {
     command = paste0('fastq-dump --fasta --split-files ', '-O read_files_directory ', id)
   } else {
     command = paste0('fastq-dump --split-files ', '-O read_files_directory ', id)