When adapting nf-core code, I realized that some modules declare their output paths using single-quoted strings (e.g. path('*.txt')), while others use double-quoted strings (like path("*.txt")). When adapting the code, this leads to inconsistencies:

Within single quoted outputs, process variables (such as meta.id) cannot be referenced using the usual mechanism ${meta.id}. This makes the code significantly harder to adapt, since using this reference mechanism in single-quoted strings leads to a (not very helpful) "Output file not found" error. I also have not found any helpful information on how to debug this problem, so it took quite some time to fix. Changing output declarations to double-quoted strings everywhere would not bring any disadvantages I'm aware of, but just enable better adaptability because the usual reference mechanism for nextflow process variables with `$' could be used in all output declarations.

Especially the inconsistent use of both single- and double-quoted strings in the different modules makes no sense. I would therefore propose to change all output path declarations to double-quoted strings.

PR checklist

• [ x] This comment contains a description of changes (with reason).
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  • For subworkflows:
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