code: def get_input_ext(self, input_file):
          
          if input_file.endswith(".bam"):
              input_ext = ".bam"
          elif input_file.endswith(".fastq.gz") or input_file.endswith(".fq.gz"):
              input_ext = ".fastq.gz"
          elif input_file.endswith(".fastq") or input_file.endswith(".fq"):
              input_ext = ".fastq"
          else:
              errmsg = "'{}'; this pipeline can only deal with .bam, .fastq, " \
                       "or .fastq.gz files".format(input_file)
              raise UnsupportedFiletypeException(errmsg)
          return input_ext
docs: Get the extension of the input_file. Assumes you're using either
          .bam or .fastq/.fq or .fastq.gz/.fq.gz.