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fmalmeida / bacannot

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
https://bacannot.readthedocs.io/en/latest/
GNU General Public License v3.0
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Split out the config profiles #43

Closed abhi18av closed 2 years ago

abhi18av commented 2 years ago

This PR addresses the discussion done in https://github.com/fmalmeida/bacannot/issues/37

fmalmeida commented 2 years ago

Hi @abhi18av,

Thanks for the contribution. I just have two considerations:

  1. In the config file you created and changed, still refers to the version v2.4. So it has a few conflicts with the new nextflow.config avaliable in v3.0. I believe this happens mainly in the docker.config.
  2. Would not be better to instead of using only: ìncludeConfig { 'conf/custom.config' }, to use includeConf { "$projectDir/conf/custom.config" } to make sure if the user copies the config to another directory to edit it, it doesn't complain about the file not existing?
abhi18av commented 2 years ago

Also, instead of master would you prefer we make a develop branch so that the untested code doesn't directly go into a release?

fmalmeida commented 2 years ago

Also, instead of master would you prefer we make a develop branch so that the untested code doesn't directly go into a release?

Perfect, I was going to suggest that. To wrap up everything first in a develop branch, then test it, and finally create a release.

fmalmeida commented 2 years ago

Things looked ready, so I merged the PR.

abhi18av commented 2 years ago

Thanks @fmalmeida!

(Apologies to late movement, I generally start open source work when the office hours are done)