comparison fastq_dump_pe.Rmd @ 3:b70047273f38 draft default tip

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit b212086a85c4d1e62e0d0c0e77b6f3fcabea04ef-dirty

2:58d48d1157ed

# download and extract reads
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' == 'No') {
    command = paste0('fastq-dump --fasta --split-files ', '-O read_files_directory ', id)
  } else {
    command = paste0('fastq-dump --split-files ', '-O read_files_directory ', id)
  }
  # fastq-dump command

3:b70047273f38

# download and extract reads
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 --split-files ', '-O read_files_directory ', id)
  } else {
    command = paste0('fastq-dump --split-files ', '-O read_files_directory ', id)
  }
  # fastq-dump command