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

[replikation]

maybe there is a way to just remove the ".fastq.gz" or ".fastq" ? because with basename the .fastq remains in the sample names

[replikation]

https://stackoverflow.com/questions/17676562/get-file-extension-for-special-cases-like-tar-gz

[hoelzer]

But then we should also cover .fq, .fq.gz ... on the other hand it's not the worst when the sample names still have the .fq extension but the pipeline still runs through ;) just if we miss some weired file end

[MarieLataretu]

because with basename the .fastq remains in the sample names

True, haven't thought about that.

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Here a code snippet for the sanity check

Channel
    .from('Hello','Hola','Ciao')
    .tap {all} // to conserve the original channel
    .collect()
    .map{ it -> [it.size(), it.unique().size()]}
    .subscribe onNext: { 
        assert it[0] == it[1]
    }

[replikation]

ping @DataSpott