feat: Strict syntax compatibility to enable better error reporting

[fellen31]

Closes #29, by providing the minimum requirements for enabling strict syntax when developing locally.

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).

[fevac]

Awesome thanks a lot! Is this also fixing the last requirement on the linked issue ’Fix strict syntax errors identified by the Nextflow language server’ ? I don't think I understand what the Nextflow language server is

[fellen31]

Awesome thanks a lot! Is this also fixing the last requirement on the linked issue ’Fix strict syntax errors identified by the Nextflow language server’ ? I don't think I understand what the Nextflow language server is

Yes, there seems to be no incompatibilities with strict syntax for oncorefiner, i.e. the pipeline runs fine with strict syntax enabled. You can use the Nextflow language server in for example VS code for syntax highlighting, diagnostics, hover hints etc.

You do have some things that could be fixed, but they are not major issues so Nextflow will still run with these problems in strict mode:

[fellen31]

Updated the changelog, I'll let you just take one more look before I merge to make sure it looks ok to you!

[kristinebilgrav]

Wow, thanks! 🌟

[fevac]

🚀