Add option for custom child-template repo

[ewels]

In some cases, people want to use the nf-core template and associated best practices (and updates), but constantly need to apply the same set of modifications when creating new pipelines. In this situation, it would be nice to be able to supply a "child template" that overwrites specific desired template files, and/or adds additional ones.

Template overrides are a pretty standard mechanism, see examples such as mkdocs, MultiQC and more.

Workflow should be:

1. Create a new repository for the custom template. Add any files that you want to overwrite.
   • For example, if you want a custom readme but everything else the same, create just a README.md file and nothing else
2. Run nf-core create --template https://github.com/myorg/mytemplate
3. The create command generates a pipeline as normal. It then renders the custom repo template afterwards, and copies these generated files on top of the vanilla pipeline output.
4. The template git repo is noted in .nf-core.yml so that the same process can be repeated for pipeline syncs (and even linting?)

Will need additional docs to describe the various template variables that are available for use, such as {{ name }} etc.

[awgymer]

This would be really useful for templating custom documentation for non-nf-core users.

A potential bonus feature would be allowing extra variables supplied by e.g. --extra_vars vars.json or something.

[mirpedrol]

This can be done now with the customizable template and the usual nf-core pipelines create command, can I close the issue?

[awgymer]

The explicit request I had that led to the creation of the original issue was that I wanted to be able to supply a physical override file/text that would replace content in e.g. the template README.md as opposed to simply being able to further refine what I included in the template.

As I understand it (when I last used v3.2) the template is more customisable but I there is still no possibility to inject extra/different template code that is not already an option as part of the template?

The use-case was mainly for non-nf-core pipelines so that you could more easily generate new pipelines with some additional boilerplate that your organisation might want

[github-actions]

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