comparison fastq_dump_se.Rmd @ 6:4c84d748da08 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit c9517f0b061cdca3b79678d9a2620e1e43115d42-dirty

5:a2ba5619f51b

sra_accessions = strsplit(gsub(',', ' ', 'SRA_ACCESSION'), ' ')[[1]]
sra_accessions = sra_accessions[sra_accessions != '']
# loop through SRA accessions to download and extract reads.
for(id in sra_accessions) {
  if(FORMAT == 'fasta') {
    command = paste0('fastq-dump --fasta ', id, ' -O read_files_directory')
  } else {
    command = paste0('fastq-dump ', id, ' -O read_files_directory')
  }
  system(command = command)
}
```

6:4c84d748da08

sra_accessions = strsplit(gsub(',', ' ', 'SRA_ACCESSION'), ' ')[[1]]
sra_accessions = sra_accessions[sra_accessions != '']
# 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 ', id)
  } else {
    command = paste0('fastq-dump ', '-O read_files_directory ', id)
  }
  print(command)
  #system(command = command)
}
```