Feature/nextflow upgrade 23 10 0

[BasMonkey]

Refactor of the in- and output variables so that the workflows can be run with Nextflow 23.10.0

[ellendejong]

Wow, amazing effort to add the val() qualifier everywhere, I approve these changes.

Some changed I would like to see:

• Long input or output tuples/lines (aka >127 characters)
• Inconsistency in whitespaces

I do see some inconsistencies in use of whitespaces. Sometimes a whitespace is added:
tuple (.....) vs tuple(...)

And there are some whitespaces before the closing brackets:
tuple(emit: fake) vs tuple ( emit: fake )

and whitespaces after a comma:
val(a),val(b), val(c) vs val(a), val(b), val(c) vs val(a),val(b),val(c)

Could you fix these inconsistencies as well to tuple(val(a), val(b), emit: fake)?

Did you check whether deprecated functions/operators are used anywhere?
https://www.nextflow.io/docs/latest/dsl1.html#channels
https://www.nextflow.io/docs/latest/dsl1.html#operators

[melferink]

Ok!