Maxime U Garcia

I think for now, this is the documentation: https://nf-co.re/sarek/3.4.0/docs/output#ngscheckmate I'm assigning @SPPearce to this issue

But you're totally right, `NGSCHECKMATE` requires `bcftools mileup` to run beforehand

I don't see anything for NGSCheckMate in https://nf-co.re/sarek/3.4.0/docs/usage, but I feel it'll be more helpful there than in https://nf-co.re/sarek/3.4.0/docs/output

Looking good

> I think this needs #1359 I think #1359 needs reviewing

> Hi, thank you for the review. FYI I currently don't have the time to work on this. I'll fix things later. No worries, we're getting a release ready, so...

can you try passing this to the sarek command line: `--cnvkit_reference /path/to/my_reference.cnn`

try with `--intervals` cf: https://nf-co.re/sarek/3.3.2/parameters#intervals

Check https://nf-co.re/sarek/dev/parameters, and be sure to check the show hidden on the right hand side to see all parameters.

The way I see it, if samples are unique (or at least sample/lane combination is unique). We can indeed have patient as optional. And in that case, output could be...