install subworkflows from nf-side

[maxulysse]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/references branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[mashehu]

Nf-core pipelines should only use nf-core or local modules and subworkflows

[maxulysse]

nf-core pipelines should only use nf-core or local modules and subworkflows

I know, and it won't be released in this state.
Still I need these functionalities for properly testing and implementing this pipeline properly.

I need things that are not in nf-core yet, and I do need these modules to be patched, as we (maintainers) still need to agree on proper handling on meta maps for references.
So as I need to be able to install subworkflows in pipeline, I am doing this for now, and will push it all to the nf-core/modules repo once done.

[mashehu]

Why not make them local first?

[maxulysse]

Why not make them local first?

I want to install these subworkflows and related modules the proper way in other pipelines for POCs.
And I don't want to copy local modules + local subworkflows 3 times everytime I update a single thing.

Consider that the nf-side/modules repo is currently the local versions of modules and subworkflows.
I will only use this before the release, and never merge any of these in any other dev branch in any pipelines.