search

KosinskiLab / AlphaPulldown

https://doi.org/10.1093/bioinformatics/btac749
GNU General Public License v3.0
218 stars 49 forks source link

Instructions how to update AP snakemake #433

Open jkosinski opened 1 month ago

jkosinski commented 1 month ago

Could you add, perhaps here: https://github.com/KosinskiLab/AlphaPulldown/blob/e35bf48f96308b02464738a777482ee2226c7032/README.md?plain=1#L269 what to do if a user has:

  1. deployed the pipeline with snakedeploy deploy-workflow
  2. edited config.yaml and added the list files
  3. run the pipeline and sth did not work (eg. bug or whatever and then we fixed the AP and then the user wants to
  4. update the AP snakemake and re-run in the same folder and reusing the previous config.yaml

From the provided instruction, I would just re-run snakedeploy deploy-workflow but would they work and not delete my config and list files?

(I am exactly in this situation right now ;-)

DimaMolod commented 1 month ago

I think if you use --branch main, you just re-run without even re-deploying. And if you use some release tag, you'll need to re-deploy to the new folder using the new tag (given there is one after we fixed a bug) and then copy the config.yaml file into the new config folder. Is that correct, @maurerv?

maurerv commented 1 month ago

Things should be stable before you deploy :)

Running snakedeploy will always remove and fetch all files that are included in the particular tag. So your changes to config.yaml and sample_sheet.csv will be overwritten