Adjusted to new strict syntax of nextflow version 26.04

[DataSpott]

With Nextflow version 26.04, the strict syntax is further enforced.
Applied a fix to all processes/modules (see below). Additionally, introduced "USER" as new
params.variable in the nextflow.config to use it in workflow profiles.

Fix-description:
In consequence, a process only knows about variables once the input block is introduced.
This results in a problem with publishDir, which typically uses variables such as ${name} to describe paths and patterns.
E.g:

process ShowError{
    publishDir "${params.output}/path/to/${name}", mode: 'copy', pattern: "${name}"
    
    input:
        tuple val(name), path(file)
    ...
}

A simple fix is to put the publishDir-strings with yet-undefined variables in closures (curly brackets "{}") so they are interpreted at runtime:

process ShowError{
    publishDir { "${params.output}/path/to/${name}" }, mode: 'copy', pattern: { "${name}" }
    
    input:
        tuple val(name), path(file)
    ...
}

[replikation]

the min version also needs to be updated or?