Genome Annotation in MAGs workflows: Change default values for some Bakta parameters

[bebatut]

In the Genome Annotation in MAGs workflows, the default value for Keep original contig header is No.
It would be better to change it to Yes, so original names are kept and it simplified downstream analyses (e.g. extraction of subsequences).

@SantaMcCloud could you address this issue? Thanks a lot

[bebatut]

I check other Bakta parameters. We should also probably set the Metagenome mode to Yes in the MAGs workflows

[SantaMcCloud]

I can make these chnages yes. Should i check all MAGs WF or do you have some specific in mind?

[bebatut]

Probably all MAGs WF where Bakta is run. Thanks a lot

[SantaMcCloud]

@bebatut i did check all the MAGs WF and i only found one WF where bakta is used. Bakta is in a sub-WF where i will open a PR to update the first parameter to yes and the other will be added via input.

After the PR with the sub-WF is merged i will open the PR for the MAG WF to be updated.

[SantaMcCloud]

Or @mvdbeek is it possible to update the sub-WF without updating it in IWC? Since the sub-WF is a IWC WF so only the MAG WF will get access to the update sub-WF.

I hope i wrote it so it is understandable sorry if not!

[mvdbeek]

I guess I don't understand 😅, you want to update a workflow without updating a workflow ?

[SantaMcCloud]

I want to update a MAG WF which has an IWC WF as a step build in which contain bakta as a step. So to make the chnages to bakta do i have to update the IWC WF first and after the merge i can update the MAG WF or can i make the whole change in the MAG WF .ga file without updating the IWC WF so that when other people use the IWC WF the never have the updated bakta version of it

[mvdbeek]

You can update what needs updating. You can update more than one workflow if necessary. Does that answer your question ?

[SantaMcCloud]

yes thank you and sorry for the confused question

[SantaMcCloud]

#1326