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@tfalkarkea , I've been working on a number of file naming issues and I think the best approach is to do as much as possible in conf/modules.config. There's a saveAs attribute in the publishDir part that can be used to set the file name. Hopefully, I'll make a PR on my parts today.
Description of feature
We need to avoid that MultiQC gets overwritten if there are several runs with different combinations of assembler and ORF caller
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