# HG changeset patch
# User mingchen0919
# Date 1528817384 14400
# Node ID 586c5cf90861580dc6780571bff6aae7a9e299c1
# Parent  9dabaecf12ff900345bf509cdf382c7535adf751
planemo upload for repository https://github.com/feltus/BDSS

diff -r 9dabaecf12ff -r 586c5cf90861 rmarkdown_report.Rmd
--- 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)
     }
     
 }