Merge pull request #118 from seqeralabs/migrate-to-nf-core-utils

Migrate to nf core utils

Author: edmundmiller

.github/CONTRIBUTING.md

@@ -16,8 +16,8 @@ If you'd like to write some code for seqeralabs/nf-aggregate, the standard workf
 1. Check that there isn't already an issue about your idea in the [seqeralabs/nf-aggregate issues](https://github.com/seqeralabs/nf-aggregate/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [seqeralabs/nf-aggregate repository](https://github.com/seqeralabs/nf-aggregate) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
-4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
-5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
+4. Update `nextflow_schema.json` for any new or changed parameters.
+5. Submit a Pull Request against `main` and wait for the code to be reviewed and merged
 
 If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
 
@@ -26,13 +26,6 @@ If you're not used to this workflow with git, you can start with some [docs from
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
 
-### Lint tests
-
-`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
-To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint <pipeline-directory>` command.
-
-If any failures or warnings are encountered, please follow the listed URL for more documentation.
-
 ## Patch
 
 :warning: Only in the unlikely and regretful event of a release happening with a bug.
@@ -53,21 +46,21 @@ If you wish to contribute a new step, please use the following coding standards:
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new parameters to `nextflow.config` with a default (see below).
-5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
+5. Add any new parameters to `nextflow_schema.json` with help text.
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test in the `tests` directory.
-9. Add a description of the output files to `docs/output.md`.
+9. Update any user-facing docs touched by the change.
 
 ### Default values
 
 Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`.
 
-Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`.
+Once there, update `nextflow_schema.json` to match.
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Set sensible defaults for process CPUs, memory, and time close to the workflow or module that owns them.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
@@ -78,14 +71,6 @@ Please use the following naming schemes, to make it easy to understand what is g
 - initial process channel: `ch_output_from_<process>`
 - intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
 
-### Nextflow version bumping
-
-If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]`
-
-### Images and figures
-
-For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
-
 ## GitHub Codespaces
 
 This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
@@ -94,7 +79,6 @@ To get started:
 
 - Open the repo in [Codespaces](https://github.com/seqeralabs/nf-aggregate/codespaces)
 - Tools installed
-  - nf-core
   - Nextflow
 
 Devcontainer specs:

.github/PULL_REQUEST_TEMPLATE.md

@@ -6,20 +6,15 @@ Many thanks for contributing to seqeralabs/nf-aggregate!
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
-Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
-
 Learn more about contributing: [CONTRIBUTING.md](https://github.com/seqeralabs/nf-aggregate/tree/main/.github/CONTRIBUTING.md)
 -->
 
 ## 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 - have you followed the pipeline conventions in the [contribution docs](https://github.com/seqeralabs/nf-aggregate/tree/main/.github/CONTRIBUTING.md)
-- [ ] Make sure your code lints (`nf-core pipelines lint`).
+- [ ] If you've added a new tool, parameter, or workflow path, update the relevant docs.
 - [ ] 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>`).
-- [ ] Usage Documentation in `docs/usage.md` is updated.
-- [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.
 - [ ] `README.md` is updated (including new tool citations and authors/contributors).

.github/workflows/clean-up.yml

@@ -12,9 +12,9 @@ jobs:
     steps:
       - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
         with:
-          stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
-          stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
-          close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
+          stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by a maintainer. Remove the stale label or add a comment, otherwise this issue will be closed in 20 days."
+          stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by a maintainer. Remove the stale label or add a comment if it is still useful."
+          close-issue-message: "This issue was closed because it was tagged as awaiting-changes or awaiting-feedback and then remained stale for 20 days."
           days-before-stale: 30
           days-before-close: 20
           days-before-pr-close: -1

.github/workflows/linting.yml

@@ -84,7 +84,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "24.04.2"
+          - "25.10.0"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false

.github/workflows/nf-test.yml

@@ -1,6 +1,6 @@
 # nf-aggregate
 
-Nextflow pipeline to aggregate metrics across Seqera Platform pipeline runs. nf-core template based (v3.3.0.dev0).
+Nextflow pipeline to aggregate metrics across Seqera Platform pipeline runs.
 
 ## Architecture
 

.nf-core.yml

@@ -1,9 +1,5 @@
 # seqeralabs/nf-aggregate: Citations
 
-## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
-
-> 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. PubMed PMID: 32055031.
-
 ## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)
 
 > 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.

AGENTS.md

@@ -1,11 +1,9 @@
 # seqeralabs/nf-aggregate
 
 [![GitHub Actions CI Status](https://github.com/seqeralabs/nf-aggregate/actions/workflows/ci.yml/badge.svg)](https://github.com/seqeralabs/nf-aggregate/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/seqeralabs/nf-aggregate/actions/workflows/linting.yml/badge.svg)](https://github.com/seqeralabs/nf-aggregate/actions/workflows/linting.yml)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -19,7 +17,7 @@ The pipeline fetches run data from the Seqera Platform API and generates benchma
 
 ## Prerequisites
 
-- [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html#installation) >=23.10.0
+- [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html#installation) >=25.10.0
 - Account in [Seqera Platform](https://seqera.io/platform/)
 - [Access token](https://docs.seqera.io/platform/23.3.0/api/overview#authentication) which is your personal authorization token for the Seqera Platform CLI. This can be created in the user menu under **Your tokens**. Export the token as a shell variable directly into your terminal if running the pipelie locally. You will not need to set this if running the pipeline within the Seqera Platform as it will automatically be inherited from the executing environment.
 
@@ -108,12 +106,4 @@ nf-aggregate was written by the Scientific Development team at [Seqera Labs](htt
 
 ## Citations
 
-This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
-
-You can cite the `nf-core` publication as follows:
-
-> **The nf-core framework for community-curated bioinformatics pipelines.**
->
-> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
->
-> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
+See [CITATIONS.md](CITATIONS.md).

CITATIONS.md

@@ -4,7 +4,7 @@ Auto-loaded by Nextflow at pipeline startup. Available in workflow/process scrip
 
 ## SeqeraApi.groovy
 
-nf-boost `request()` wrappers for Seqera Platform API. Used in the v2 benchmark path — called directly in `map{}` operators, no container needed.
+Plain `java.net.URL.openConnection()` HTTP client for Seqera Platform API. Used in the v2 benchmark path — called directly in `map{}` operators, no container needed.
 
 ### Methods
 
@@ -32,6 +32,6 @@ Calls `/orgs` → finds org by name → calls `/orgs/{orgId}/workspaces` → fin
 
 ### Gotchas
 
-- Uses `nextflow.boost.BoostFunctions` — requires `nf-boost` plugin
+- Uses plain `java.net.URL.openConnection()` for HTTP requests — no external plugin dependency
 - Runs in the Nextflow head JVM, not in a container process
 - Network errors throw `RuntimeException` which will fail the pipeline