Strict syntax health - Part 1

[kubranarci]

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/variantbenchmarking 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).

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[kubranarci]

@nf-core-bot fix linting

[georgiakes]

Looks good overall. Just 2 things I wanted to flag—let me know if these should be addressed now or are planned for a follow-up:

1. Replace all Channel factories with channel - Currently we've only updated the version channels and input channels declared at the top of the script.

2. Remove version channels for subworkflows with only nf-core modules - Since the modules have the topics channel we do not need a versions channel

[kubranarci]

Yes, actually my overall plan is to get 1&2 until we release version 1.5. Yet, I realised first this PR getting too long and second some nf-core modules doesnt comply strict syntax for now. Therefore, I will update those nf-core modules and come back with part 2 to complete 1&2. Thanks for the overview @georgiakes !

[georgiakes]

Okay then! We follow up with these changes on part 2 :)