Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump

diff fastq_dump_se.Rmd @ 2:58d48d1157ed draft

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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 16:53:21 -0400
parents 1a11c4fd13d0
children b70047273f38
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--- a/fastq_dump_se.Rmd	Tue Oct 10 20:48:29 2017 -0400
+++ b/fastq_dump_se.Rmd	Mon Oct 16 16:53:21 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' == 'fasta') {
+  if('FORMAT' == 'No') {
     command = paste0('fastq-dump --fasta ', '-O read_files_directory ', id)
   } else {
     command = paste0('fastq-dump ', '-O read_files_directory ', id)