This release brings exciting new features focused on nf-test integration, test dataset management and modules from different repositories in subworkflows. As always, if you have any problems or run into any bugs, reach out on the #tools slack channel.

Highlights

New nf-core infrastructure members

This release marks the first release with contributions from two new nf-core infrastructure members. @JulianFlesch and @ningyuxin1999 are doing their PhDs at QBiC and will be working 50% for the nf-core infrastructure team.

nf-test for pipelines

Approximately 2 years ago, nf-core started using nf-test to test modules and subworkflows. Since then, there has been a huge work form the community to switch all nf-core components from testing with pytest, to testing with nf-test.

During the 2024 Barcelona Hackathon in October, a group of contributors worked on a proof of concept to add pipeline-level nf-test tests. After this first attempt, other pipeline maintainers started to join in, and started implementing nf-test to their pipelines. With some of the most used pipelines in nf-core, and others, having implemented these tests, it is time for nf-core/tools to catch-up, and add this to the pipeline template.

To improve the robustness of nf-core pipeline testing workflows and help developers catch issues early in the development process, we’ve added pipeline-level nf-tests to the pipeline template.

This can be seen in four new template files:

nf-test.config       # The pipeline-level nf-test configuration file
tests/
├── .nftignore       # ignored files for nf-test
├── default.nf.test  # The default test for the pipeline, mirroring the setup in config/test.config
└── nextflow.config  # The nextflow configuration for the pipeline tests

Additionally, we changed the CI setup to use nf-tests with sharding to speed up the testing process. This means good-bye to good old ci.yml and hello to nf-test.yml.

nf-test test tests/ --profile=+<docker/singularity/conda etc.>

skip_features:
    - "nf-test"

lint:
    files_exist:
        - ".github/workflows/nf-test.yml"
        - ".github/actions/get-shards/action.yml"
        - ".github/actions/nf-test/action.yml"
        - "nf-test.config"
        - "tests/default.nf.test"
    nf_test_content: False

To lower the load on our GitHub runners (especially during hackathons), we will use self-hosted runners for nf-test GitHub Actions. These are automatically set up for all nf-core repository. See our recent blog post on self-hosted GitHub Actions runners to learn more about our setup.

Big thanks to everyone who contributed to this big addition to the nf-core template, especially @maxulysse, @adamrtalbot, @SateeshPeri, @GallVp and @edmundmiller for testing and tinkering, especially with the GitHub Actions. 🙌

New nf-core test-datasets command

Our newest infrastructure-team member @JulianFlesch has added a new CLI command to make it easier to find and integrate data sets from the nf-core/test-datasets repository.

nf-core test-datasets list
nf-core test-datasets search

This new command provides streamlined functionality for:

• Dataset discovery: Easily search and explore available test datasets

  List all datasets for a specific branch:

  

  Search for a specific term and get more detailed information about the dataset:

  

• Dataset integration: Easily use test datasets in your pipeline by providing the download URL

  

  or the path used in the pipeline test files:

  

See the full documentation here: test-datasets list, and test-datasets search.

Installing subworkflows with components from different remotes

Previously, when installing a subworkflow from a custom repository, all of its components had to be from the same repository. This release adds support for subworkflows that use components from multiple repositories.

Thanks to João Cavalcante for implementing this feature and to everyone who provided feedback, especially Arthur Gymer and Matthieu Muffato.

Changelog

You can find the complete changelog and technical details on GitHub.

Getting help to update your pipeline template

All the template changes are listed in the Template section of the changelog. Below, we have collected the most common merge conflicts that you may find and how to resolve them.

Video walkthrough

.editorconfig

The .editorconfig file was deleted - The same functionality was replaced by adding the trailing-whitespace and end-of-file-fixer hooks, and with additional settings in .prettierrc.yml.

Resolution

You can delete the .editorconfig file and make sure that you accept the changes in .pre-commit-config.yaml.

nf-test files

If your pipeline added nf-test before this template update, you might see some conflicts in the following files:

• .github/actions/nf-test/action.yml
• .github/workflows/nf-test.yml
• .nftignore
• tests/nextflow.config
• nf-test.config

Resolution

It is a good idea to accept the changes made by the template, since they might contain updates and bug fixes that we have found thanks to the pipelines that added nf-test before. Make sure to double-check the changes and understand them, and don’t delete any extra content that you added to your tests. If you need help, do not hesitate to reach out on slack

ci.yml

The file ci.yml was removed and replaced by nf-test.yml.

Resolution

Once you have implemented nf-test, by updating the default.nf.test file, you can safely remove this file, this is replaced by nf-test.yml.

CITATIONS.md

Resolution

If you have added additional citations, keep them!

modules.json

This file often has merge conflicts during template updates because it typically contains pipeline-specific information.

Resolution

Don’t accept the changes.

Instead, run the command nf-core modules update --all to update all nf-core module after resolving the template update conflicts. This will make sure that all modules are updated and the correct version is specified in this file.

nextflow.config

Resolution

Keep all your added parameters.

Accept the additions that come with this template update:

• We have added a new profile gpu
• We have added a new value to the errorStrategy
• The expression to include config files has changed
• nf-schema can be bumped back to 2.3.0
• If you have modified the contributors, added more tests, etc. don’t remove them.

README.md

We have replaced the Twitter badge for Bluesky and we have added an nf-core template version badge. This is one of the harder files to sync with the template, because it usually doesn’t contain any custom content.

Resolution

Accept the changes to the Twitter badge and the nf-core template version badge. Keep your Zenodo URL and your custom text.

ro-crate-metadata.json

The file ro-crate-metadata.json is updated on nf-core pipelines sync.

Resolution

Accept the changes.

GitHub Actions

In the Github Action download_pipeline.yml we have removed the pull_request_target and added a step to upload the nextflow.log file.

In all Github Actions (files inside .github/workflows) you will see several version updates.

Resolution

You can accept all version updates.

Pipeline logos

If you see changes in pipeline logos: accept them, except if you customized them.

modules.config

This file often has merge conflicts during template updates because it typically contains pipeline-specific content.

Resolution

Make sure to keep all your custom changes.

conf/base.config

We added the withLabel: process_gpu config to the base config.

Resolution

Accept the incoming gpu profile but keep your customizations.

.nf-core.yml

There might be a conflict between the different nf_core_version values.

Resolution

Accept the newer version.

3 June 2025

@mashehu

@mirpedrol