Anders Sune Pedersen

> Hmmm.. I am not certain which way the community swings when it comes to adding functionalities like generating compressing outputs in a module. Perhaps we should bring this up...

Doing some experiments on this. It seems that `bgzip` isn't available in the container that is used for hmtnote, but `gzip` is. Is it okay to use `gzip`or does it...

Aren't mulled containers causing problems and frustration from time to time? Not sure it is worthwhile.

TNseq and TNscope still not implemented :-/

This is issue no longer relevant as we don't have Sentieon's BQSR function implemented in Sarek, and we don't plan to implement it in Sarek. https://github.com/nf-core/sarek/blob/dev/docs/usage.md#qualcal-bqsr

done

done

> @asp8200 By what PR? Could you link something for reference, please? Closed by https://github.com/nf-core/modules/pull/3224

@FriederikeHanssen and @maxulysse : The vcf-file resulting from the concatenation may contain the same variant several times: ``` chr22 2123 . C G 28 PASS SNVHPOL=3;MQ=60 GT:GQ:GQX:DP:DPF:AD:ADF:ADR:SB:FT:PL 0/1:30:12:3:2:1,2:0,1:1,1:-6.9:PASS:63,0,27 chr22 3140...

We've decided that - for now - we just do concatenation of **germline** vcf-files.