Remove stale nf-core template remnants

[FloWuenne]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool, parameter, or workflow path, update the relevant docs.
• If plugin declarations changed, update CITATIONS.md, README.md, and agent/context guidance in the same PR.
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

Description

Remove stale nf-core template residue that is no longer used, including deleting the leftover .nf-core.yml file that contradicted the repository guidance.

Also align plugin documentation and future agent guidance with the actual pinned plugins in nextflow.config by:

• documenting nf-core-utils@0.4.0 and nf-schema@2.3.0 in CITATIONS.md
• calling out the pinned plugin references from README.md
• updating repo/agent context so future contributors re-check for stale nf-core-template remnants and keep plugin citations synchronized
• renaming the main CI workflow label from nf-core CI to Pipeline CI so it reflects the current repository setup

Testing

• uv run --with typer --with pyyaml --with jinja2 --with pyarrow --with pytest --with httpx pytest -v modules/local/aggregate_benchmark_report_data/tests/test_aggregate.py modules/local/normalize_benchmark_jsonl/tests/test_normalize.py modules/local/render_benchmark_report/tests/test_render.py bin/test_benchmark_report_fetch.py
• nf-test test --profile=+docker --verbose
• nextflow run . --input workflows/nf_aggregate/assets/test_benchmark.csv --generate_benchmark_report --outdir /tmp/nf-aggregate-e2e-results -profile docker
• pre-commit run --all-files

  

[FriederikeHanssen]

Don't think the utils plugin has a citation?

[maxulysse]

yeah, that's a citation for nf-core in general.

no need for that for plugins, for me the URL is enough.
I would not even put versions as it's a pain to update whenever you update the plugin.

That being said, even if this is now diverging quite a lot from standard nf-core pipeline, I would still keep a general citation to nf-core.

[FriederikeHanssen]

Thanks for adding the citation back in

[maxulysse]

minor comments, but LGTM

[FloWuenne]

OK, I moved the citation for nf-core back to a general nf-core citation and out of nf-core-utils. I agree with @maxulysse that a general nf-core citation should remain, even if the template isn't used anymore!