this has to use the -o option, not redirect to stdout in order for
    gzipping to be supported

def _cutadapt_se_cmd(fastq_files, out_files, base_cmd, data):
    """
    this has to use the -o option, not redirect to stdout in order for
    gzipping to be supported
    """
    min_length = dd.get_min_read_length(data)
    cmd = base_cmd + " --minimum-length={min_length} ".format(**locals())
    fq1 = objectstore.cl_input(fastq_files[0])
    of1 = out_files[0]
    cmd += " -o {of1_tx} " + str(fq1)
    cmd = "%s | tee > {log_tx}" % cmd
    return cmd