Mercurial > repos > mingchen0919 > aurora_bdss_sra

changeset 7:586c5cf90861 draft

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planemo upload for repository https://github.com/feltus/BDSS
author mingchen0919
date Tue, 12 Jun 2018 11:29:44 -0400
parents 9dabaecf12ff
children 6e13714671f1
files rmarkdown_report.Rmd
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/rmarkdown_report.Rmd	Tue Jun 12 11:24:08 2018 -0400
+++ b/rmarkdown_report.Rmd	Tue Jun 12 11:29:44 2018 -0400
@@ -113,7 +113,7 @@
     if(!(paste0(id, '_2.', opt$X_f) %in% list.files('pe_read_files_dir'))) {
       # this is not a paired end SRA file. The corresponding file will be deleted.
       cat(paste0(id, ' is not paired end SRA, the corresponding fastq/fasta file will deleted.'))
-      command_stdout = system(paste0('rm ', pe_dir, ' ', id, '_1.*'), intern = TRUE)
+      command_stdout = system(paste0('rm ', pe_dir, '/', id, '_1.*'), intern = TRUE)
     }
     
 }