the -c option that was forcing it to read CNF1 formatted srf files
def condor_srf_to_fastq(srf_file, target_pathname, paired, flowcell=None,
mid=None, force=False):
def condor_srf_to_fastq(srf_file, target_pathname, paired, flowcell=None,
mid=None, force=False):
- args = ['-c', srf_file, ]
if paired:
args.extend(['--left', target_pathname])
# this is ugly. I did it because I was pregenerating the target
if paired:
args.extend(['--left', target_pathname])
# this is ugly. I did it because I was pregenerating the target