Replace check_max function with resourceLimits directive

[jfy133]

Closes #2923

PR checklist

• [ ] This comment contains a description of changes (with reason)
• [ ] CHANGELOG.md is updated
• [ ] If you've fixed a bug or added code that should be tested, add tests!
• [ ] Documentation in docs is updated

[github-actions[bot]]

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Hi @jfy133,

It looks like this pull-request is has been made against the jfy133/nf-core-tools master branch. The master branch on nf-core repositories should always contain code from the latest release. Because of this, PRs to master are only allowed if they come from the jfy133/nf-core-tools dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[jfy133]

I tested locally by running the nf-core/test-pipeline example in the CI.

By adjusting --max_memory to 16, the FASTQC process that would normally get 32GB (label_medium) was indeed capped at 16 (normally it would be allocated 32)

[maxulysse]

Let's just remove params.max_* entirely 🔥

Just don't remove me please

[jfy133]

OK the tasks from the slack thread here

• [x] Remove all references to --max_* parameters
• [x] Add lint tests (so people remove the parameters)
• [x] Set new defaults in tests configs
• [ ] Update the docs on the website
  • [ ] Add warning about legacy useage
  • [ ] New docs to describe how to use new resourceDirectives
• [ ] mass update all configs on nf-core/configs
  • [ ] Keep old --max_* parameters (buit leave comment)
  • [ ] Copy vbalues to new resourcesLimits (with

[jfy133]

@nf-core-bot fix linting

[mirpedrol]

This is ready to merge, ok if we merge it @jfy133 ? We have to change the branch protection for the two pending tests, but I want to do it right before merging, otherwise it will block other PRs.

[jfy133]

Yes I think we can do but we Just have to be careful that people don't try to use dev to generate pipelines because configs won't work, I'll try and work out a mass configs PR ASAP.

Docs can come later I guess

[mirpedrol]

ok I will merge it now! It won't affect old pipelines so it should be good 👍