Maxime U Garcia

Can you share the content of `nextflow-bear.config` too?

I think `GATK_BEDTOINTERVALLIST` should cover the BED part

I agree with you, and early fail would be better in that case

`Segmentation fault` sounds bad. Any chance it works again if you resume?

Good idea, that would make sense

Looks interesting. Sounds easy enough to do. I'd like to see that in nf-core/modules first before adding to sarek. But we will definitively have a look

Adding this to the milestone for `3.2`

That's good to know, hopefully that'll be fix at the next GATK release then

> I have multiple of the same errors. Is there a way to solve it other than manually sorting the bed files? unfortunately not at the moment, but we're thinking...

we should really fix #892, that will help with the spelling of the tools