I think the manual sync docs need to be updated with the new nf-core #tools

I think the manual sync docs need to be updated wi...

Pieter Moris

11/21/2025, 2:22 PM

I think the manual sync docs need to be updated with the new

pipelines sync

instead of of

sync

command? https://nf-co.re/docs/tutorials/sync/manual_sync

Pieter Moris

11/21/2025, 2:22 PM

But I'm having trouble getting it work on an old pipeline, so maybe manual sync is not supported anymore? (`ERROR Workflow config variable

manifest.contributors

not found!`). Maybe because it's trying to jump from tools 2.13.1 to 3.5.1 🥲

Pieter Moris

11/21/2025, 2:23 PM

The pulling from an upstream nf-core repository part is also a bit confusing, since supposedly this guide is for non-nf core pipelines that were created without nf-core tools create. So what would the upstream be?

Nicolas Vannieuwkerke

11/21/2025, 2:40 PM

You should add the

manifest.contributors

section to the config to get this working. See Sarek for an example: https://github.com/nf-core/sarek/blob/9b85c0f04b5d7f279f407125a8cad6bcc2d801f5/nextflow.config#L405-L820

mashehu

11/21/2025, 2:45 PM

or try to downgrade your nf-core version to 3.0 for example and do the sync in two steps

party this 1

Pieter Moris

11/21/2025, 3:52 PM

Will give those a try, ty ! The alternative I had in mind was nuking the template branch, recreating a new one based on the latest nf-core tools, and then interactive rebasing my original changes on top of it (being careful to only add changes to the pipeline itself and not the tooling around it).

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