Use `eval` to collect version

Nextflow 24.02.0-edge brings with it two new features which should give much cleaner syntax for collecting tool versions: channel topics using topic (see https://github.com/nf-core/modules/issues/4517) and eval. They are designed to work together nicely, but are technically separate features.

• Docs for eval: https://nextflow.io/docs/latest/process.html#output-type-eval
• Blog post about eval and topic: https://nextflow.io/blog/2024/nextflow-2404-highlights.html#process-eval-outputs
• Example pipeline change: https://github.com/nf-core/fetchngs/pull/312

The blog post contains a basic example of how this can be used to collect versions:

process FASTQC {
  input:
  tuple val(meta), path(reads)

  output:
  tuple val(meta), path('*.html'), emit: html
  tuple val("${task.process}"), val('fastqc'), eval('fastqc --version'), topic: versions 

  """
  fastqc $reads
  """
}

workflow {
  Channel.topic('versions') 
    | unique()
    | collectFile(name: 'collated_versions.yml')
    | CUSTOM_DUMPSOFTWAREVERSIONS
}

Needs some thought about how we approach these changes - may be best to do a bulk change everywhere in one go, as it affects multiple code locations (modules and pipelines).

Start with the linked Nextflow eval documentation, blog example, and the existing version-collection patterns across the modules and pipelines. Identify all affected locations, then verify that the migrated outputs collect into the expected collated_versions.yml flow and that the relevant module and pipeline checks still pass.