feat: Pre-commit hook for automatic parameters documentation generation

[fellen31]

If this is something you would like to have :), this PR adds:

• Parameters documentation
• A pre-commit hook to automatically generate this via nf-core pipelines schema docs -o docs/parameters.md --force whenever nextflow_schema.json is modified.

See https://github.com/genomic-medicine-sweden/nf-core-schema-docs for more information.

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/oncorefiner 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).

[fellen31]

A good (better) alternative to this could also be the newly released nf-docs.

[beatrizsavinhas]

This looks great! Thank you for showing it to us. 🌟

I will just confirm with the rest of the team if this is something we want to add and, if so, I can come back to approve it!

[beatrizsavinhas]

@Clinical-Genomics/cancer agrees this is a good feature to add!
Thank you again @fellen31 for the suggestion and work to add it here. 🌟

[fellen31]

@Clinical-Genomics/cancer agrees this is a good feature to add! Thank you again @fellen31 for the suggestion and work to add it here. 🌟

👍 Someone with admin access to the repo should edit the expected statuses that this PR affects.

[beatrizsavinhas]

@Clinical-Genomics/cancer agrees this is a good feature to add! Thank you again @fellen31 for the suggestion and work to add it here. 🌟

👍 Someone with admin access to the repo should edit the expected statuses that this PR affects.

The required actions have been updated (since the test run was removed - ci.yml was removed with the template update in #35)!
I think that if you update your branch and resolve the conflicts, you should be able to merge! But let us know if the issue persists.

[fellen31]

@Clinical-Genomics/cancer agrees this is a good feature to add! Thank you again @fellen31 for the suggestion and work to add it here. 🌟

👍 Someone with admin access to the repo should edit the expected statuses that this PR affects.

The required actions have been updated (since the test run was removed - ci.yml was removed with the template update in #35)! I think that if you update your branch and resolve the conflicts, you should be able to merge! But let us know if the issue persists.

So it's these two that were moved into the "lint" workflow.

[beatrizsavinhas]

@Clinical-Genomics/cancer agrees this is a good feature to add! Thank you again @fellen31 for the suggestion and work to add it here. 🌟

👍 Someone with admin access to the repo should edit the expected statuses that this PR affects.

The required actions have been updated (since the test run was removed - ci.yml was removed with the template update in #35)! I think that if you update your branch and resolve the conflicts, you should be able to merge! But let us know if the issue persists.

So it's these two that were moved into the "lint" workflow.

Ah, of course! I will temporarily disable these restrictions so you can merge. And then will require the lint check instead!

[beatrizsavinhas]

The only relevant files for this PR are .prettierignore and .github/workflows/linting.yml, right? Is it possible that the rest of the changes were accidentally introduced when resolving merge conflicts after updating the branch?

[fellen31]

Oh no! Fixing in #41