Blank output with --docx --docx_template default_template.docx

[cmfield]

A Word file is produced, but none of the reported resistances in the .txt file are listed in the table. I got the template from your other repository.

This is currently with 6.3.0 (6.4.0 isn't compatible with the most recent release of pathogen profiler and I have to use versioned software), docxcompose 1.4.0, docxtpl 0.17.0 - any other relevant packages let me know.

[jodyphelan]

Hi @cmfield,

Version 6.4.1 recently came out on conda. Are you able to use this version? It also includes an improved default report.
If not I can look into v6.3.0

[cmfield]

The problem is that 6.4.0+ cause this error with pathogen-profiler 4.4.0:

Traceback (most recent call last):
  File "/mnt/data/software_stack/easybuild/software/TBProfiler/6.4.1-foss-2023a/bin/tb-profiler", line 664, in <module>
    args.func(args)
  File "/mnt/data/software_stack/easybuild/software/TBProfiler/6.4.1-foss-2023a/bin/tb-profiler", line 109, in wrapper
    func(args)
  File "/mnt/data/software_stack/easybuild/software/TBProfiler/6.4.1-foss-2023a/bin/tb-profiler", line 132, in main_profile
    rules_applied = pp.apply_rules(args.conf['rules'], variants_profile, just_make_note=True if args.implement_rules==False else False)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: apply_rules() got an unexpected keyword argument 'just_make_note'

[jodyphelan]

Oh yes it this is a new feature that was introduced in pathogen-profiler v4.5.0+.
Could you try cupdate pathogen-profiler from 4.4.0 to 4.5.1? If you are installing through conda then it should automatically install the right version of pathogen-profiler.

https://github.com/bioconda/bioconda-recipes/blob/66455fb30d0169d2539d18b339c5c8b5880b4f7a/recipes/tb-profiler/meta.yaml#L32