Closed fmalmeida closed 1 year ago
Bakta outputs are extremely similar to Prokka, however, their annotation is more reliable. Therefore, the addition seems to be very straightforward:
One thing to think is:
Recapitulating:
To add bakta it would be necessary to:
Now that pipeline has been restructured, this issue can become a reality.
Since bakta database is huge, instead of downloading and formatting with the pipeline users will have to download themselves as each system or institute will have a way to handle such massive download.
Thus, if users want to annotate and trigger bakta, they will have to simply:
--bakta_db
When using this parameter, the pipeline should automatically trigger bakta instead of prokka.
Finally, after very much time, workflow is now properly running from top to bottom when using bakta
. For release, it is now required to:
bakta
option. How to use it? What to expect?prokka
or bakta
. Check if everything is well rendered.prokka
must understand when pipeline run using additional hmm libraries for prokka
, and which ones were used (from the ones possible when building databases).bakta
, there is addional parsing of outputs that we can do to give users more information in outputs?Almost ready.
try to roll it up in the next 3 days
Something is wrong with bakta docker image. When running it, it is complaining about diamond. With some -9 exit code.
Execution tests were finished. Now building new docker images, to check whether scripts and reports are properly updated so release can be made.
Finally done 🥳
Study the best way to implement Bakta in the pipeline.
It will be nice to provide the users with the option to choose the base annotation with Prokka or Bakta, depending on their needs.
Check if it will be possible to add it.