Important! Template update for nf-core/tools v3.3.1

[maxulysse]

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
• Make sure your code lints (nf-core pipelines lint).
• 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).

[maxulysse]

Only lingering issues are:

Failed to get organization details for community in workspace showcase -- Check script '/home/runner/work/nf-aggregate/nf-aggregate/modules/local/seqera_runs_dump/functions.nf' at line: 9

@FloWuenne

[maxulysse]

BTW, I squeeze in an alphabetical sort order

[Copilot]

Pull Request Overview

This PR updates the nf-core/templates and related testing infrastructure to support nf-aggregate v3.3.1, including updates to snapshot files, configuration files, and GitHub Actions workflows. Key changes include:

• Refreshing test snapshots and updating test configurations (nf-test.config, default tests) to align with the new template.
• Updating URL references from api.tower.nf to api.cloud.seqera.io and bumping the nf-core template version.
• Introducing new workflow profiles (e.g. gpu) and adding/updating GitHub Actions workflows and custom actions for nf-test.

Reviewed Changes

Copilot reviewed 23 out of 23 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/main.nf.test.snap, tests/default.nf.test.snap, tests/default.nf.test	Updated test snapshots and assertions for consistency with v3.3.1
subworkflows/local/utils_nf_aggregate/tests/main.nf.test.snap	Updated run IDs and workspace values to the new naming scheme
ro-crate-metadata.json	Updated metadata such as datePublished and template references
nf-test.config	Modified workDir source and ignore triggers; bumped plugin version
nextflow.config	Added a GPU profile with appropriate runOptions
modules/local/seqera_runs_dump/tests/*	Updated input values to reflect domain and workspace changes
modules/local/plot_run_gantt/tests/main.nf.test, modules/local/benchmark_report/tests/main.nf.test	Updated domain URLs in test inputs
assets/multiqc_report.html, README.md	Updated URL references and nf-core template version links
.prettierrc.yml, .nf-core.yml	Minor configuration tweaks and version bumps
.github/workflows/nf-test.yml, .github/actions/*, .github/CONTRIBUTING.md	Added new nf-test workflows and custom actions; removed legacy CI workflow

Comments suppressed due to low confidence (1)

.github/workflows/ci.yml:1

• The legacy CI workflow file is removed in this PR. Please confirm that all necessary tests are now covered by the new nf-test workflow to avoid any gaps in the CI process.

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml

[maxulysse]

Still seeing Failed to get organization details for seqeralabs in workspace showcase...

[FloWuenne]

@maxulysse The new nf-test ci/cd was simply missing the env TOWER_ACCESS_TOKEN!

[maxulysse]

@maxulysse The new nf-test ci/cd was simply missing the env TOWER_ACCESS_TOKEN!

good catch 🤦