Pipeline documentation: standardisation with nf-core template architecture

[MaximilianStammnitz]

PR checklist

• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.1.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[mashehu]

Nice! I also had a quick look into the docs section: pipeline_steps.md will not be rendered on the website, but can maybe merged into README.md

[mashehu]

@nf-core-bot fix linting

[mashehu]

automerge will not work because of the required pre-commit linting step.

[MaximilianStammnitz]

ah, I see – though it feels like all the available merge options also require auto?

[mashehu]

I disabled the required CI steps for now, so you should be able to merge it. will be enabled after you release.