PathoFact integration

• how should we approach this?
• just add plasflow and the AMR prediction into "our" workflow?
• or use the git submodule option and refer to PathoFact?

changed the description

added To Do label

changed milestone to %Greatness achieved

• @valentina.galata: the file was too big, so it's been uploaded here: https://drive.google.com/file/d/1ubq5pUhPgHPQxdcQmEGC0jj7kNRgKTLt/view?usp=sharing
• 5bb54bf8 - Rscript used to generate figure PathoFact figure

I think we should not include data in the repo. Anything that can be generated from result files should be excluded. I will remove files which were generated by me (these are small anyway). Regarding the rest: there should be rules to generate them. I think I make a new issue for that.

PathoFact figure script: Okay, I will have a look at it.

• okay with me.
• Thank you!

marked this issue as related to #28 (closed)

marked this issue as related to #29 (closed)

Closing because PathoFact is in review and will undergo some changes. Plasmid and AMR prediction is done by other tools.

closed

added Analysis label and removed To Do label