Add AGENTS.md file and the related template feature

[itrujnara]

This PR adds AGENTS.md to the pipeline template. This is currently intended as a place to discuss the draft of the file. Please DO NOT MERGE until the file has been manually tested in a few pipelines.

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

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.07%. Comparing base (db5e3bb) to head (24113e9).
⚠️ Report is 42 commits behind head on dev.

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[mashehu]

before we add this, I would like to see it in several pipelines. To check that everything works as expected

[itrujnara]

@mashehu sure, that is the plan in the RFC. I have opened this as draft so that people can leave comments on the file and/or copy it to pipelines.

[ewels]

Please also include in the pipeline lint test files_unchanged: https://nf-co.re/docs/nf-core-tools/api_reference/4.0.2/pipeline_lint_tests/files_unchanged

[itrujnara]

Lint test added, can someone help with the CI errors?

[mashehu]

you need to update the snapshots. for the test_create_app, I can give it a try. the other one is a simple nf-test snapshot of pipeline created with just that feature

[itrujnara]

@nf-core-bot update snapshots

Resolved