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add misc items and shoutout ro crate contributors
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mashehu committed Dec 9, 2024
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This release comes with some new features and smaller pipeline template, which shouldn't cause too much of a head-ache.
As always, if you have any problems or run into any bugs, reach out on the [#tools slack channel](https://nfcore.slack.com/archives/CE5LG7WMB).

# New Features
# Highlights

- Pipelines generated with nf-core/tools now come with their own Research Object (RO) Crate.
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.
More information can be found [here](https://www.researchobject.org/ro-crate/).
Thanks to [Phil Ewels](https://github.com/ewels), [Stian Soiland-Reyes](https://github.com/stain) and [Simone Leo ](https://github.com/simleo) for kicking off this effort and providing useful feedback!

:::note
This RO Crate describes the pipeline as a whole, not pipeline runs.
For that kind of provenance, use the new [nf-prov plugin](https://github.com/nextflow-io/nf-prov), which is currently in development.
:::

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

- `nf-core pipelines download` supports now ORAS container URIs.
Previously, you needed to use a `https://` prefix, but thanks to the work by [@MatthiasZepper](https://github.com/MatthiasZepper") we can now use the `oras://` prefix.
- `main` as default release branch for pipelines. With this release we extended the template and tooling to support either `main` or `master` as the default branch for pipelines.
You can follow the progress of this transition on the [pipeline health page](/pipeline_health).
- The newly added `nf-core subworkflows patch` command allows 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 comes with the expanded contributors section in the manifest (see [manifest docs](https://www.nextflow.io/docs/latest/reference/config.html#manifest) for details)

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