Add dummy configs for all missing configs

[jfy133]

This is for allowing us to uncomment out the part in the pipeline template.

I wonder if it just works 'as is' or if we have to add an explicit profile or not... ideas @maxulysse ?

[jfy133]

Not tested because on train

[mashehu]

If you want I can write a github action which periodically checks https://nf-co.re/pipeline_names.json and creates that.

[mashehu]

One thing I find sub-optimal: we now have conf/pipeline/ and pipeline/. too easy to confuse the two, imo

[maxulysse]

One thing I find sub-optimal: we now have conf/pipeline/ and pipeline/. too easy to confuse the two, imo

both have different usage, but I see your point

[mashehu]

yes, different usage and same name is never good

[jfy133]

If you want I can write a github action which periodically checks https://nf-co.re/pipeline_names.json and creates that.

That would be awesome

[jfy133]

Should I wait for the GHA @mashehu before merging? But otherwise I will prepare the tools template to uncomment the relevant code, and update our new-project-guidance

[mashehu]

yes, I will add the GHA to this PR. Any chance we can use a different name than pipeline/ for the placeholders?

[jfy133]

yes, I will add the GHA to this PR. Any chance we can use a different name than pipeline/ for the placeholders?

No I don't think so. It's already embedded in existing pipelines for a while, so if we changed it would break compatibility with old releases. @maxulysse correct me if I'm wrong

[mashehu]

okay, GHA is there. as usual need to really test it in production (I ran it locally with act and it looked fine, but we will see). Left some testing code in it, so we will need a clean-up PR after this one is merged and the workflow has been tested

[jfy133]

Looks good to me @mashehu !

If you can both review: https://github.com/nf-core/tools/pull/2936/ and re-review this one, then i will merge this PR and shortly after the tools one