This release comes with some new features and smaller pipeline template, which shouldn’t cause too much of a headache. As always, if you have any problems or run into any bugs, reach out on the #tools slack channel.

Highlights

Research Object (RO) Crates in nf-core pipelines

RO Crate is an open-source standard which we use to describe our pipelines and their components in a structured way and helps with automated provenance tracking. In our case, it describes all files that are in the pipeline template, as well as the pipeline authors, besides some general metadata. More information about RO Crates can be found here. Thanks to Phil Ewels, Stian Soiland-Reyes and Simone Leo for kicking off this effort and providing useful feedback!

If you want to update the RO Crate for your pipeline, run nf-core pipelines rocrate (automatically run with nf-core pipelines sync).

For more information about the command and how it generates the RO Crate, see the docs.

ORAS container URI support in nf-core pipelines download

Previously, you needed to use a https:// prefix, but thanks to the work by @MatthiasZepper we can now use the oras:// prefix. This requires singularity to be installed on your system.

main as optional default branch

With this release we extended the template and tooling to support either main or master as the default release branch for pipelines.

If you want to use the main branch in your pipeline, make sure to set defaultBranch = main on the manifest section from the nextflow.config file. Afterwards, you can change the GitHub repository default branch to main.

Then, you can run nf-core pipelines sync again. This will automatically change all the required links from master to main.

nf-core subworkflows patch

This new commandallows you to patch subworkflows in the same way as you would patch modules.

Miscellaneous

• When running nf-core pipelines create you can now toggle all pipelines features on and off with one switch.

• The template now includes an expanded contributors section in the manifest, as introduced in Nextflow 24.10.0 for details. We added a new TODO nf-core comment, so please add the missing information to these fields. Completing these fields will allow us for example to improve the data in the RO crate, especially the ORCID.

  The newly added fields are:

  manifest {
      contributors = [
          [
              name: '',
              affiliation: '',
              email: '',
              github: '',
              contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor')
              orcid: ''
          ],
      ]
  }

• We moved includeConfig 'conf/modules.config' next to includeConfig 'conf/base.config' to not overwrite tests profiles configurations. Thanks to Louis Le Nézet for adding this change.

Possible merge conflicts and how to resolve them

.nf-core.yml

We started to clean null values from the .nf-core.yml file, so if you get something like the following, you can accept this change.

<<<<<<< nf-core-template-merge-3.1.0
+ nf_core_version: 3.1.0
=======
- nf_core_version: 3.0.1
- org_path: null
>>>>>>> dev

Resolution

You can just accept the changes that don’t include null values, i.e. the ones coming from nf-core-template-merge-3.1.0.

Published on

10 December 2024

Written by

@mashehu

@mirpedrol

@ewels