diff rmarkdown_report.Rmd @ 8:6e13714671f1 draft

planemo upload for repository https://github.com/feltus/BDSS

--- a/rmarkdown_report.Rmd	Tue Jun 12 11:29:44 2018 -0400
+++ b/rmarkdown_report.Rmd	Tue Jun 12 11:41:41 2018 -0400
@@ -110,11 +110,11 @@
     cat('----convert SRA to fastq/fasta------\n')
     command_stdout = system(command, intern = TRUE)
     write(command_stdout, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/fastq-dump.log.txt'), append = TRUE)
-    if(!(paste0(id, '_2.', opt$X_f) %in% list.files('pe_read_files_dir'))) {
-      # this is not a paired end SRA file. The corresponding file will be deleted.
-      cat(paste0(id, ' is not paired end SRA, the corresponding fastq/fasta file will deleted.'))
-      command_stdout = system(paste0('rm ', pe_dir, '/', id, '_1.*'), intern = TRUE)
-    }
+    # if(!(paste0(id, '_2.', opt$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)
+    # }
     
 }