From 40bf8f66793643c1665b4bc1b3f30bb0e67e40fc Mon Sep 17 00:00:00 2001 From: Cursor Agent Date: Wed, 22 Apr 2026 12:49:59 +0000 Subject: [PATCH 1/2] Remove stale nf-core template remnants Co-authored-by: Florian Wuennemann --- .github/PULL_REQUEST_TEMPLATE.md | 1 + .github/workflows/ci.yml | 4 ++-- .nf-core.yml | 35 -------------------------------- .seqera/context/PIPELINE.md | 2 +- AGENTS.md | 7 ++++--- CITATIONS.md | 12 +++++++++++ README.md | 2 +- 7 files changed, 21 insertions(+), 42 deletions(-) delete mode 100644 .nf-core.yml diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 9c801348..c670b9d8 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.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 `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] `CHANGELOG.md` is updated. diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index fb02371d..60fe57dd 100644 --- a/.github/workflows/ci.yml +++ b/.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: diff --git a/.nf-core.yml b/.nf-core.yml deleted file mode 100644 index 41f8392d..00000000 --- a/.nf-core.yml +++ /dev/null @@ -1,35 +0,0 @@ -lint: - base_config: false - files_exist: false - files_unchanged: false - modules_config: false - multiqc_config: false - nextflow_config: - - custom_config - - manifest.homePage - - manifest.name - - process.cpus - - process.memory - - process.time - pipeline_name_conventions: false - schema_lint: false - template_strings: - - bin/benchmark_report_template.html - - assets/AGENTS.md - nf_test_content: - - tests/nextflow.config -nf_core_version: 3.3.1 -repository_type: pipeline -template: - author: SciDev Team - description: Pipeline to aggregate pertinent metrics across pipeline runs on the Seqera Platform. - force: false - is_nfcore: false - name: nf-aggregate - org: seqeralabs - outdir: . - skip_features: - - ci - - igenomes - - nf_core_configs - version: 0.7.0 diff --git a/.seqera/context/PIPELINE.md b/.seqera/context/PIPELINE.md index 6d3bc024..49fd82d3 100644 --- a/.seqera/context/PIPELINE.md +++ b/.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 diff --git a/AGENTS.md b/AGENTS.md index f21e2a50..0c4b15f1 100644 --- a/AGENTS.md +++ b/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 diff --git a/CITATIONS.md b/CITATIONS.md index f1825ae6..13fbe30b 100644 --- a/CITATIONS.md +++ b/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) diff --git a/README.md b/README.md index b49a4fda..47a510b9 100644 --- a/README.md +++ b/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. From 5a866f82979a74bd61c8a981db5ccebfb02296ca Mon Sep 17 00:00:00 2001 From: FloWuenne Date: Wed, 22 Apr 2026 09:53:41 -0400 Subject: [PATCH 2/2] =?UTF-8?q?=F0=9F=93=9D=20docs(citations):=20promote?= =?UTF-8?q?=20nf-core=20to=20top-level=20citation=20section?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Move the nf-core framework citation out of the plugin entry and into its own section, consistent with the Nextflow citation above it. Co-Authored-By: Claude --- CITATIONS.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/CITATIONS.md b/CITATIONS.md index 13fbe30b..e8834730 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -4,12 +4,14 @@ > 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. +## [nf-core](https://www.nature.com/articles/s41587-020-0439-x) + +> 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. + ## 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)