code: def _guess_cmd_name(self, cmd):
          
  
          # zcat to bowtie
          if cmd[0] == 'zcat' and 'bowtie' in cmd:
              return 'bowtie'
          # samtools
          if cmd[0] == 'samtools':
              return ' '.join(cmd[0:2])
          # java (eg. picard)
          if cmd[0] == 'java':
              jars = [s for s in cmd if '.jar' in s]
              return os.path.basename(jars[0].replace('.jar', ''))
          return cmd[0]
docs: Manually guess some known command names, where we can
          do a better job than the automatic parsing.