docs: def skewer(
              self, input_fastq1, output_prefix, output_fastq1,
              log, cpus, adapters, input_fastq2=None, output_fastq2=None):
          """
          Create commands with which to run skewer.
  
          :param str input_fastq1: Path to input (read 1) FASTQ file
          :param str output_prefix: Prefix for output FASTQ file names
          :param str output_fastq1: Path to (read 1) output FASTQ file
          :param str log: Path to file to which to write logging information
          :param int | str cpus: Number of processing cores to allow
          :param str adapters: Path to file with sequencing adapters
          :param str input_fastq2: Path to read 2 input FASTQ file
          :param str output_fastq2: Path to read 2 output FASTQ file
          :return list[str]: Sequence of commands to run to trim reads with
              skewer and rename files as desired.
          """
  
          pe = input_fastq2 is not None
          mode = "pe" if pe else "any"
          cmds = list()
          cmd1 = self.tools.skewer + " --quiet"
          cmd1 += " -f sanger"
          cmd1 += " -t {0}".format(cpus)
          cmd1 += " -m {0}".format(mode)
          cmd1 += " -x {0}".format(adapters)
          cmd1 += " -o {0}".format(output_prefix)
          cmd1 += " {0}".format(input_fastq1)
          if input_fastq2 is None:
              cmds.append(cmd1)
          else:
              cmd1 += " {0}".format(input_fastq2)
              cmds.append(cmd1)
          if input_fastq2 is None:
              cmd2 = "mv {0} {1}".format(output_prefix + "-trimmed.fastq", output_fastq1)
              cmds.append(cmd2)
          else:
              cmd2 = "mv {0} {1}".format(output_prefix + "-trimmed-pair1.fastq", output_fastq1)
              cmds.append(cmd2)
              cmd3 = "mv {0} {1}".format(output_prefix + "-trimmed-pair2.fastq", output_fastq2)
              cmds.append(cmd3)
          cmd4 = "mv {0} {1}".format(output_prefix + "-trimmed.log", log)
          cmds.append(cmd4)
          return cmds