Remove deprecated syntax

[maxulysse]

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[ewels]

From the Nextflow docs:

In Nextflow versions prior to 22.03.0-edge, you must enable DSL2 explicitly in order to use it. You can either set the feature flag in your pipeline script:

nextflow.enable.dsl=2

So as long as we are specifying a minimum version above that it should be good to remove.

[maxulysse]

From the Nextflow docs:

In Nextflow versions prior to 22.03.0-edge, you must enable DSL2 explicitly in order to use it. You can either set the feature flag in your pipeline script:

nextflow.enable.dsl=2

So as long as we are specifying a minimum version above that it should be good to remove.

https://github.com/nf-core/tools/blob/dsl2_enabled/nf_core/pipeline-template/nextflow.config#L261

[maxulysse]

@mirpedrol any idea about the failures?

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 76.03%. Comparing base (53a04db) to head (6dd57df).

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