Change return type of listFiles() from Path[] to List<Path>

[bentsherman]

Fix #6152

Functions in the standard library that return an array instead of a list are problematic because arrays don't have all the same functionality of a list. For example, a Path[] can't be accepted by process path inputs which expect a Collection<Path>.

Should be effectively non-breaking for Nextflow users, but let's see if it breaks anything in the runtime...

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[pditommaso]

This can introduce breaking changes in third parties pipelines. Not sure the change is worth

[bentsherman]

The problem is that these methods are documented in the Nextflow language as returning a list instead of an array:

list() -> List<String>

Returns the first-level elements (files and directories) of a directory as a list of strings.

listFiles() -> List<Path>

Returns the first-level elements (files and directories) of a directory as a list of Paths.

Because arrays don't exist in the Nextflow type system

It looks like everyone is wrapping listFiles() with an extra call like .toList() or as List<Path> in order to use it like an actual list. So for them it should not be breaking, it will just enable additional functionality

[pditommaso]

I understand the point about type system, however the array type has been used to keep aligned with the File version in Groovy SDK, until there isn't a clear boundary between nextflow and groovy and java API this change little.

Secondly and even this kind of changes are extremely annoying for users because may introduce subtle bugs hard to detect, and confuse agents.

If this change is really needed better to deprecated, document and induce and new API

[bentsherman]

the array type has been used to keep aligned with the File version in Groovy SDK

@pditommaso what method are you talking about? I can't find anything in the Groovy or Java SDK that returns a path array

[bentsherman]

Never mind, found it: https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/io/File.html#listFiles()