code: def set_align_options(p):
      
      p.add_option("--bwa", default="bwa", help="Run bwa at this path")
      p.add_option("--rg", help="Read group")
      p.add_option("--readtype",
                   choices=("pacbio", "pbread", "ont2d", "intractg"),
                   help="Read type in bwa-mem")
      p.set_cutoff(cutoff=800)
docs: Used in align() and batch()