code: def main(self):
          
          # 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()
docs: Run the methods in the correct order for pipelines