Runs reformat.sh on the FASTQ files. If a CalledProcessError arises, do not proceed with the assembly of
        these files

def validate_fastq(self):
        """
        Runs reformat.sh on the FASTQ files. If a CalledProcessError arises, do not proceed with the assembly of
        these files
        """
        logging.info('Validating FASTQ files')
        with progressbar(self.metadata) as bar:
            for sample in bar:
                # Tiny files can pass the validation tests - ensure that they don't
                size = os.path.getsize(sample.general.fastqfiles[0])
                if size >= 1000000:
                    # Try to run reformat.sh on the reads - on any errors try to run repair.sh
                    try:
                        out, err, cmd = bbtools.validate_reads(forward_in=sample.general.fastqfiles[0],
                                                               returncmd=True)
                        write_to_logfile(out, err, self.logfile, sample.general.logout, sample.general.logerr,
                                         None, None)
                    except CalledProcessError:
                        # Set the file names for the reformatted and repaired files
                        outputfile1 = os.path.join(sample.general.outputdirectory, '{}_reformatted_R1.fastq.gz'
                                                   .format(sample.name))
                        repair_file1 = os.path.join(sample.general.outputdirectory, '{}_repaired_R1.fastq.gz'
                                                    .format(sample.name))
                        if len(sample.general.fastqfiles) == 2:
                            outputfile2 = os.path.join(sample.general.outputdirectory, '{}_reformatted_R2.fastq.gz'
                                                       .format(sample.name))
                            repair_file2 = os.path.join(sample.general.outputdirectory, '{}_repaired_R2.fastq.gz'
                                                        .format(sample.name))
                        else:
                            outputfile2 = str()
                            repair_file2 = str()
                        # Use reformat.sh to repair the reads. If this fails, discard the sample from the analyses
                        try:
                            logging.warning('Errors detected in FASTQ files for sample {sample}. '
                                            'Please check the following files for details {log} {logout} {logerr}. '
                                            'The pipeline will use reformat.sh to attempt to repair issues'
                                            .format(sample=sample.name,
                                                    log=self.logfile,
                                                    logout=sample.general.logout,
                                                    logerr=sample.general.logerr))
                            if not os.path.isfile(outputfile1):
                                # Run reformat.sh
                                out, err, cmd = bbtools.reformat_reads(forward_in=sample.general.fastqfiles[0],
                                                                       forward_out=outputfile1,
                                                                       returncmd=True)
                                write_to_logfile(out, err, self.logfile, sample.general.logout, sample.general.logerr,
                                                 None, None)
                                # Run repair.sh (if necessary)
                                if outputfile2:
                                    out, err, cmd = bbtools.repair_reads(forward_in=outputfile1,
                                                                         forward_out=repair_file1,
                                                                         returncmd=True)
                                    write_to_logfile(out, err, self.logfile, sample.general.logout,
                                                     sample.general.logerr, None, None)
                            # Ensure that the output file(s) exist before declaring this a success
                            if os.path.isfile(outputfile1):
                                # Update the fastqfiles attribute to point to the repaired files
                                sample.general.fastqfiles = [repair_file1, repair_file2] if repair_file2 \
                                    else [outputfile1]
                        except CalledProcessError:
                            # The file(s) can be created even if there is STDERR from reformat.sh
                            if os.path.isfile(outputfile1) and outputfile2:
                                try:
                                    out, err, cmd = bbtools.repair_reads(forward_in=outputfile1,
                                                                         forward_out=repair_file1,
                                                                         returncmd=True)
                                    write_to_logfile(out, err, self.logfile, sample.general.logout,
                                                     sample.general.logerr, None, None)
                                    # Update the fastqfiles attribute to point to the repaired files
                                    sample.general.fastqfiles = [repair_file1, repair_file2] if repair_file2 else \
                                        [repair_file1]
                                except CalledProcessError:
                                    # Write in the logs that there was an error detected in the FASTQ files
                                    write_to_logfile('An error was detected in the FASTQ files for sample {}. '
                                                     'These files will not be processed further'.format(sample.name),
                                                     'An error was detected in the FASTQ files for sample {}. '
                                                     'These files will not be processed further'.format(sample.name),
                                                     self.logfile,
                                                     sample.general.logout,
                                                     sample.general.logerr,
                                                     None,
                                                     None)
                                    # Update metadata objects with error
                                    self.error(sample, 'fastq_error')
                            else:
                                # Write in the logs that there was an error detected in the FASTQ files
                                write_to_logfile('An error was detected in the FASTQ files for sample {}. '
                                                 'These files will not be processed further'.format(sample.name),
                                                 'An error was detected in the FASTQ files for sample {}. '
                                                 'These files will not be processed further'.format(sample.name),
                                                 self.logfile,
                                                 sample.general.logout,
                                                 sample.general.logerr,
                                                 None,
                                                 None)

                                # Update metadata objects with error
                                self.error(sample, 'fastq_error')
                else:
                    # Update metadata objects with error
                    self.error(sample, 'files_too_small')
        # Print the metadata to file
        metadataprinter.MetadataPrinter(self)