Implementation of nextflow strict syntax

[DataSpott]

With the latest nextflow update, we want to migrate the workflow to their new strict syntax model, which is described here: https://www.nextflow.io/docs/latest/updating-syntax.html

Due to our already good structure, these are primarily minor changes. Nevertheless, we need to incorporate some structural changes, e.g. inputs and help messages need to become part of the workflow section. I will incorporate them and inform everybody before we merge the changes into the main branch. If you have any suggestions please let me know.

[replikation]

@DataSpott please add nextflowVersion = '!>=24.10.4' to the configs manifest section.

[replikation]

full run with 40 samples runs fine