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docs: adding missing pipelines cli prefix#4257

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simojoe wants to merge 2 commits into
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docs-update-nf-core-pipelines-call
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docs: adding missing pipelines cli prefix#4257
simojoe wants to merge 2 commits into
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docs-update-nf-core-pipelines-call

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@simojoe

@simojoe simojoe commented Jun 14, 2026

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Closes nf-core/tools#3287

I used the breaking changes in the CLI commands from the blog post of release 3.0.0. I only modified information that was from 3.0.0 and more.

https://nf-co.re/blog/2024/tools-3_0_0

This is my first naïve contribution to the website repository, please let me know if I skipped some relevant steps.

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@mashehu mashehu left a comment

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thanks for these fixes. just some small suggestions

This first "vanilla" commit which is identical to the output from the templating tool is important, as it allows us to keep your pipeline in sync with the base template in the future.
A full description of the file structure and all files created in the initial pipeline setup can be found [here](https://nf-co.re/docs/contributing/pipelines/pipeline_file_structure).
See the [nf-core syncing docs](https://nf-co.re/docs/tutorials/sync/overview) for more information on how the syncing works.
See the [nf-core pipelines sync docs](https://nf-co.re/docs/tutorials/sync/overview) for more information on how the syncing works.

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Suggested change
See the [nf-core pipelines sync docs](https://nf-co.re/docs/tutorials/sync/overview) for more information on how the syncing works.
See the [nf-core syncing docs](https://nf-co.re/docs/tutorials/sync/overview) for more information on how the syncing works.

we mean the process not the actual command here 🙂

| `nf-core download{:bash}` | `nf-core pipelines download{:bash}` |
| `nf-core create-params-file{:bash}` | `nf-core pipelines create-params-file{:bash}` |
| `nf-core create{:bash}` | `nf-core pipelines create{:bash}` |
| `nf-core lint{:bash}` | `nf-core pipelines lint{:bash}` |

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what was wrong with this line?

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Documentation shows the old commands without pipelines prefix

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