Refactor empty meta map pattern in main.nf

[pinin4fjords]

Description

There are approximately 17 occurrences of the empty meta map pattern `[ [:], ... ]` in `main.nf` where channels are constructed with an empty map as the meta element. For example:

```groovy
ch_fasta = Channel.value([ [:], file(params.fasta, checkIfExists: true) ])
```

This pattern is used because many nf-core modules expect a `[meta, file]` tuple, but at the pipeline level there's no meaningful per-sample metadata for reference files.

Proposal

Consider refactoring to reduce repetition, for example:

• A helper function like `refChannel(path)` that wraps the pattern
• Or using Nextflow's native value channels with map operators

This would improve readability and reduce the chance of inconsistencies.

Context

Raised during review of PR #1717 (3.23.0 release).