Update to nextflow strict syntax

[d4straub]

Nextflow is changing eventually to stricter syntax, described in https://www.nextflow.io/docs/latest/strict-syntax.html. This PR solves all errors (but not warnings) regarding this strict syntax for Nextflow extension for Visual Studio Code, version 1.2.0.
Following this stricter syntax allows using the full potential of the Nextflow language support plugin and it should make the pipeline code (more) future proof.

Specific changes:

• all local modules had their when statement removed (this causes most of the file changed here)
• for loops were replaced with .each
• .anyMatch was replaced with .any
• all variables had a def added
• switch was replaced by if/else (only in nf-core module vsearch/usearchglobal ) via Update vsearch/usearchglobal to strict syntax modules#8333
• workflows/ampliseq.nf had the params & channel creation moved into workflow
• Implicit closure parameter it was added as it -> in all local workflows and subworkflows [this is not causing an error, but it alone is deprecated]

There are no functional changes whatsoever in this PR, only syntax improvements.

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/ampliseq 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).

[d4straub]

@nf-core-bot fix linting

[d4straub]

Unfortunately all latest-everything tests are expected to fail because nf-schema 2.3.0 is not compatible with the most recent nextflow edge release.

[ggabernet]

Looks good to me

[ggabernet]

Unfortunately all latest-everything tests are expected to fail because nf-schema 2.3.0 is not compatible with the most recent nextflow edge release.

The fix is to downgreat [email protected] to [email protected] in the nextflow.config for now

[d4straub]

Thanks!
Yes, I will downgrade nf-schema in a separate PR.