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Add googlebatch config docs and update default_private_ip to false #805

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@hnawar hnawar commented Nov 22, 2024


name: googlebatch
about: Update to existing googlebatch config

Please follow these steps before submitting your PR:

  • If your PR is a work in progress, include [WIP] in its title
  • Your PR targets the master branch
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Steps for adding a new config profile:

  • Add your custom config file to the conf/ directory
  • Add your documentation file to the docs/ directory
  • Add your custom profile to the nfcore_custom.config file in the top-level directory
  • Add your custom profile to the README.md file in the top-level directory
  • Add your profile name to the profile: scope in .github/workflows/main.yml
  • OPTIONAL: Add your custom profile path and GitHub user name to .github/CODEOWNERS (**/<custom-profile>** @<github-username>)

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jfy133 commented Nov 25, 2024

@nf-core-bot fix linting

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Hi @hnawar ,

I started an internal discussion about this when you first opened but then had sick kits along the way.

So on onehand, being a newcomer to this config, I personally don't particularly like all these extra parameters that are being added (e.g. --project_id, --location, --use_spot etc). These aren't supported by nf-core pipelines so every user will get a warning of an 'unknown parameter' at the beginning of every run with no validation or check it's working correctly. So even though you say they are 'required' parameters, no pipeline will actually check these.

Given it seems to be that much of this config requires a lot of user configuration, I would rather a user make their own custom config for each project/run if this is the case.

The other issue is because Nextflow config resolution particularly is problematic when it comes to the params scope, meaning whatever is set in this config could be entirely overwritten if someone provides an additional custom config - so we like to avoid as much 'flexible' scopes of the pipeline as possible.

However as a compromise as this config has already been around for a while, could you please update the config to tell validation to ignore those parameters so users at least don't get warnings of confusing 'unknown' parameters, e.g.

image

but with all parameters.

Pinging @maxulysse, @edmundmiller and @nvnieuwk who I discussed this with

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