Remove stale nf-core template remnants

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,6 +14,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/seqeralabs/n
 - [ ] 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.

.github/workflows/ci.yml

@@ -1,5 +1,5 @@
-# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
-name: nf-core CI
+# This workflow runs the pipeline tests and benchmark-report checks
+name: Pipeline CI
 on:
   pull_request:
   release:

.seqera/context/PIPELINE.md

@@ -7,7 +7,7 @@
 - **Repository:** [https://github.com/seqeralabs/nf-aggregate](https://github.com/seqeralabs/nf-aggregate)
 - **Latest released version:** 0.7.0 (2025-05-05)
 - **Current branch:** `edmundmiller/seqera-context` (active development)
-- **Plugins:** [nf-schema@2.3.0](mailto:nf-schema@2.3.0) (param validation, samplesheet parsing), [nf-boost@0.6.0](mailto:nf-boost@0.6.0) (request(), JSON helpers)
+- **Plugins:** `nf-core-utils@0.4.0` (Conda checks, params dump, software version helpers), `nf-schema@2.3.0` (param validation, samplesheet parsing)
 - **Required env:** `TOWER_ACCESS_TOKEN` for API-mode runs
 
 ## Architecture

AGENTS.md

@@ -23,8 +23,8 @@ input CSV (id, workspace, group, logs, fusion)
 
 ## Plugins
 
-- `nf-schema@2.3.0` — param validation, samplesheet parsing
-- `nf-boost@0.6.0` — `request()`, `fromJson`/`toJson` for API calls
+- `nf-core-utils@0.4.0` — utility helpers such as Conda checks and software-version reporting
+- `nf-schema@2.3.0` — param validation and samplesheet parsing
 
 ## Env Requirements
 
@@ -62,7 +62,8 @@ uv run --with typer --with pyyaml \
 - `commit.gpgsign` must be true (SSH signing via 1Password)
 - RTK `buildOutputFiltering` / `testOutputAggregation` can swallow nf-test output — disable to debug
 - **Nextflow `include` statements in `main.nf` must be single-line.** `adamrtalbot/detect-nf-test-changes@v0.0.3` (used by CI) parses include lines and crashes on multi-line blocks. Write `include { A ; B ; C } from '...'` not multi-line blocks.
-- **No `.nf-core.yml` in this repo.** The nf-core pipelines lint CI job has been removed because it depends on `.nf-core.yml` which was dropped. Do not re-add the `nf-core` job to `.github/workflows/linting.yml` without also restoring `.nf-core.yml`.
+- **Repository hygiene:** `.nf-core.yml` should stay absent unless nf-core linting is intentionally restored alongside the required config. When changing CI, docs, or plugin declarations, remove stale nf-core-template remnants and keep labels/docs accurate.
+- **Plugin references must stay synchronized.** If `nextflow.config` plugin entries change, update `CITATIONS.md`, `README.md`, and agent/context files in the same change so pinned plugins such as `nf-core-utils` and `nf-schema` are cited consistently.
 
 ## Cursor Cloud specific instructions
 

CITATIONS.md

@@ -4,6 +4,18 @@
 
 > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
 
+## Nextflow plugins used by this pipeline
+
+- [`nf-core-utils@0.4.0`](https://github.com/nf-core/nf-utils)
+
+  > Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x.
+
+  Software source pinned in `nextflow.config`: `https://github.com/nf-core/nf-utils` (version `0.4.0`).
+
+- [`nf-schema@2.3.0`](https://github.com/nextflow-io/nf-schema)
+
+  Software source pinned in `nextflow.config`: `https://github.com/nextflow-io/nf-schema` (version `2.3.0`).
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

README.md

@@ -143,4 +143,4 @@ nf-aggregate was written by the Scientific Development team at [Seqera Labs](htt
 
 ## Citations
 
-See [CITATIONS.md](CITATIONS.md).
+See [CITATIONS.md](CITATIONS.md), including the pinned plugin references for `nf-core-utils@0.4.0` and `nf-schema@2.3.0` used by this pipeline.