I'm noticing that the VariantBenchmarking pipeline fails if you're comparing a test and query file of the same name. I imagine the underlying issue is actually one that nextflow should address but has anyone run into this issue before? Building some automation to test releases will regularly require doing comparisons between files of the same name so I imagine others have run into this before.

Interesting

Can you send me an example log? I think you can change prefix for query to overcome this. This is probably happening as test and truth are combined for benchmarking tools, and when they both are the same name nextflow processes are "throwing same channel error" I think I have never encounter this as I always use different names 😅 I will think of a way of way around this

Thanks for the help Kubra. I'll get that to you in a little bit.