Enable the ITOL annotations in the tb-profiler command

[abhi18av]

As discussed in our meeting on 13-June-2024, we realised that the default behavior for the command had changed and now we explicitly need to enable the generation of annotations.

I did a test run and for some reason the presence of Mcanetti is raising an issue.

  Traceback (most recent call last):
    File "/usr/local/bin/tb-profiler", line 583, in <module>
      args.func(args)
    File "/usr/local/bin/tb-profiler", line 269, in main_collate
      tbp.collate_results(args)
    File "/usr/local/lib/python3.10/site-packages/tbprofiler/collate.py", line 149, in collate_results
      generate_itol_config(rows,drugs,args.prefix)
    File "/usr/local/lib/python3.10/site-packages/tbprofiler/collate.py", line 178, in generate_itol_config
      writer.write(lineage_outfile)
    File "/usr/local/lib/python3.10/site-packages/itol_config/interfaces/colour_strip.py", line 33, in write
      O.write("%s\t%s\n" % (index,self.colour_lookup[value]))
  KeyError: 'M.canetti'
  Cleaning up after failed run
             ERROR                                                  tb-profiler:59

                      ################################# ERROR
                      #######################################

                      This run has failed. Please check all
                      arguments and make sure all input files
                      exist. If no solution is found, please open
                      up an issue at
                      https://github.com/jodyphelan/TBProfiler/issu
                      es/new and paste or attach the
                      contents of the error log
                      (joint.major_variants.errlog.txt)

                      #############################################
                      ##################################

  INFO:    Cleaning up image...

[abhi18av]

As of a0e54af , the iTOL annotations have been restored as a normal output of drug_resistance folders (major/minor/structural )