I think I am misunderstanding something very basic about

file.name

and

file.baseName

: I am trying to do something very simple: if a file is zipped (bz2, xz, gz) I want to remove the extension, if it is not, then keep it.

outname = ["xz", "bz2", "gz"].contains("${infile.extension}") ? "${infile.baseName}" : "${infile.name}"
outfile = task.ext.prefix ? "${task.ext.prefix}.gz" : "${outname}.gz"

This works ok for unzipped files, they receive

.gz

in addition to their original extension, but something that is

vcf.gz

becomes

vcf.gz.gz

. It seems like baseName does not remove the extension, but why?

what is your

task.ext.prefix

set as?

it should be unset

it should be a string already according to the docs... https://docs.seqera.io/nextflow/reference/stdlib-types#extension-string what nextflow version are you using

I am using 25.10.4