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
def skewer ( self , input_fastq1 , output_prefix , output_fastq1 , log , cpus , adapters , input_fastq2 = None , output_fastq2 = None ) : 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
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.