Wolfgang Maier

Ah, OldSnpEff does not even have a `self.effects['Transcript_BioType']` (hence the now failing test). Also, SnpEff.coding seems to suffer from the same `consequence` vs `consequences` mix-up. I could fix those, but...

Ok, so this was a bit more work than I intended originally, but I cleaned up the class hierarchy of Effect and its subclasses quite a bit and fixed a...

The thing is though that after all this cleanup work it becomes apparent that most of it won't help Gemini because from https://github.com/arq5x/gemini/blob/5db2e52ae4aee413a8780df538565c90a38e4b11/gemini/gemini_load_chunk.py#L498 onwards Gemini only uses the top impact...

yeah, I guess you can argue like that, which would mean that the docs need an update.

The counter argument would be one of practicality: what's documented - `is_exonic = 1` if any effect on any transcript is an exonic one - is just very hard to...

yeah, #1352 is another case where an option became non-functional with that refactoring. @simonbray rescued `--update_test_data` via https://github.com/galaxyproject/planemo/pull/1232/files#r885840184, but `--failed` and `--job_output_files` that also got handled through `run_in_config` were less...

Since an aspect of `--skip-venv` handling was also part of `run_in_config`, I am now wondering whether the broken behavior of that option that I mentioned in https://github.com/galaxyproject/planemo/issues/1343#issuecomment-1384194149 is also related.

Cool! My own ordering by importance of these options is very similar: `--update_test_data` == `--failed` > `--job_output_files` > `--skip-venv` for the last, I don't have any actual use and would...

> > ./tools/ena_upload/ena_upload.xml: #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')): > > that is fine Is it? How is it guaranteed that the job handler can access that file?

> shouldn't the symlink be replaced with a command for it? There shouldn't be a reason to use os.system there, it's just unnecessary cheetah addition. Think so too, plus I...