Update to Nextflow 25.04

This PR updates the fetchngs pipeline to use Nextflow 25.04: - **Use `eval` outputs, topic channels to collect tool versions.** Simplify the collection of tool versions, removes lots of boilerplate from processes and workflows. Topic channels are out of preview in 25.04, so they can be used without the feature flag. - **Use the `output` block to publish outputs.** Publish outputs at workflow level by publishing channels. Use the index file feature to generate the samplesheet. Workflow outputs are still in preview as of 25.04, but I do not expect the syntax to change much at this point. It should accept the same parameters and produce the exact same outputs as before.