Catch identical filenames

[MarieLataretu]

I suggest to change simpleName to baseName here: https://github.com/replikation/poreCov/blob/9ba98fe38d666508fa7dd0bd16d4accc5fe36a4b/poreCov.nf#L183 (and potentially somewhere else) to avoid problems with file names with more than one ..

Else or in addition a sanity check for identical file names would be good.

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Context: https://www.nextflow.io/docs/latest/script.html#check-file-attributes