Mercurial > repos > mingchen0919 > aurora_bdss_sra
changeset 6:9dabaecf12ff draft
planemo upload for repository https://github.com/feltus/BDSS
| author | mingchen0919 |
|---|---|
| date | Tue, 12 Jun 2018 11:24:08 -0400 |
| parents | a1dfadeb3b59 |
| children | 586c5cf90861 |
| files | rmarkdown_report.Rmd |
| diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/rmarkdown_report.Rmd Tue Jun 12 11:13:54 2018 -0400 +++ b/rmarkdown_report.Rmd Tue Jun 12 11:24:08 2018 -0400 @@ -103,9 +103,9 @@ write(command_stdout, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/bdss-download.log.txt'), append = TRUE) # convert .sra to .fastq/.fasta if(opt$X_f == 'fasta') { - command = paste0('fastq-dump --fasta --split-files -O ',pe_dir, ' ', id, '.sra') + command = paste0('fastq-dump --fasta --split-files -O ', pe_dir, ' ', id, '.sra') } else { - command = paste0('fastq-dump --split-files -O ',pe_dir, ' ', id, '.sra') + command = paste0('fastq-dump --split-files -O ', pe_dir, ' ', id, '.sra') } cat('----convert SRA to fastq/fasta------\n') command_stdout = system(command, intern = TRUE) @@ -113,7 +113,7 @@ if(!(paste0(id, '_2.', opt$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_read_files_dir/', id, '_1.*'), intern = TRUE) + command_stdout = system(paste0('rm ', pe_dir, ' ', id, '_1.*'), intern = TRUE) } }