code: def _cutadapt_pe_cmd(fastq_files, out_files, quality_format, base_cmd, data):
      
      fq1, fq2 = [objectstore.cl_input(x) for x in fastq_files]
      of1, of2 = out_files
      base_cmd += " --minimum-length={min_length} ".format(min_length=dd.get_min_read_length(data))
      first_cmd = base_cmd + " -o {of1_tx} -p {of2_tx} " + fq1 + " " + fq2
      return first_cmd + "| tee > {log_tx};"
docs: run cutadapt in paired end mode