Any ideas why I'm still getting test failures here, when I've moved the location of a file in a template, and I think(?) I've updated all the paths accordingly in the template etc? https://github.com/nf-core/tools/pull/3903

I think you got the path wrong. See my comment

Looks better, but still a few errosr 😞

It might be related to

nf_core/pipelines/create/template_features.yml

and adding the

docs/CONTRIBUTING.md

there?

documentation:
      skippable_paths:
        - "docs"
      short_description: "Add documentation"
      description: "Add documentation to the pipeline"
      help_text: |
        This will add documentation markdown files where you can describe your pipeline.
        It includes:
        - docs/CONTRIBUTING.md: A contributing guide to help others contribute to your pipeline.
        - docs/README.md: A README file where you can describe the structure of your documentation.
        - docs/output.md: A file where you can explain the output generated by the pipeline
        - docs/usage.md: A file where you can explain the usage of the pipeline and its parameters.

        These files come with an exemplary documentation structure written.
      linting:
        files_exist:
          - "docs/CONTRIBUTING.md"
          - "docs/output.md"
          - "docs/README.md"
          - "docs/usage.md"
      nfcore_pipelines: False
      custom_pipelines: True
      default: true

I'll try pushing to my branch!

Yup, much simpler to recreate than to meddle with the CI.

OK one final error...

okay, found the problem. You added a

nf-core TODO

and that is removed in this check (to avoid linting errors because of that), but is still in the template. Don't remember at the moment, why this isn't a problem in other files (hopefully tomorrow-morning–me remembers (or @Júlia Mir))

Oh jeez

I was trying to fix this error, I thought the solution was to lint the file partially (only the template content must be there but it can contain additional text), but this doesn't work either because of the TODO comment that will have to be removed

Ah yeah that would make sense, the idea is you could modify the bottom of the file too...

but why does the README.md and usage.md etc. work even though they also have TODO statements?

we don't lint those

Is there anything for me to do at the moment?

no don't worry 😄 if you all agree I will remove this file form the linting and they you should be good to go

And there isn't 'unchanged first half' checjk?

that's the partial-linting julia tried before

Ah I see

oh, to be more correct, partial linting allows appendices to the template, (we could add a linting end marker, but probably easier to just drop linting it for now)

OK fair enough

everything looks ✅ now 🙂

Woohoo! thank you very much @Júlia Mir @mashehu @Chris Hakkaart @Matthias Zepper!