Mercurial > repos > mingchen0919 > rmarkdown_fastq_dump
diff fastq_dump_pe.Rmd @ 13:66bc1016ec2a draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit affb362adeb095389646b0c51738d24c2de3838d-dirty
author | mingchen0919 |
---|---|
date | Wed, 27 Sep 2017 16:54:07 -0400 |
parents | d330ce2d4663 |
children | dcd0e0b6fcaf |
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--- a/fastq_dump_pe.Rmd Wed Sep 27 16:49:22 2017 -0400 +++ b/fastq_dump_pe.Rmd Wed Sep 27 16:54:07 2017 -0400 @@ -31,16 +31,11 @@ # loop through SRA accessions to download and extract reads. for(id in sra_accessions) { if('FORMAT' == 'fasta') { - command = paste0('fastq-dump --fasta ', '-O read_files_directory ') + command = paste0('fastq-dump --fasta --split_files ', '-O read_files_directory ') } else { - command = paste0('fastq-dump ', '-O read_files_directory ') + command = paste0('fastq-dump --fastq --split_files ', '-O read_files_directory ') } - if('SPLIT_FILES' == TRUE) { - command = paste0(command, '--split_files ', id) - } else { - command = paste0(command, id) - } print(command) system(command = command) }