def main(self):
        """
        Run the methods in the correct order for pipelines
        """
        # Find the target files
        self.targets()
        # Use bbduk to bait the FASTQ reads matching the target sequences
        self.bait()
        # If desired, use bbduk to bait the target sequences with the previously baited FASTQ files
        if self.revbait:
            self.reversebait()
        # Run the bowtie2 read mapping module
        self.mapping()
        # Use samtools to index the sorted bam file
        self.indexing()
        # Parse the results
        self.parsebam()