Refactor to adhere to language server

[FriederikeHanssen]

Refactoring code to adhere to the language server

WIP:

• config if/else statements: I assume we need a lot of closers in the publishDir if that is possible
• Several modules need updating upstream
• still need to address warnings

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/sarek 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: 3.0.2.
Please update your pipeline to the latest version.

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[maxulysse]

meta map?

[maxulysse]

ie:

ext.prefix = { "${meta.id}.${meta.prefix}" }

and:

path: { "${params.outdir}/preprocessing/${meta.publish_path}/${meta.id}/" },

[maxulysse]

it can be removed

[maxulysse]

do we need this with the profile spark?