Friederike Hanssen

awesome 🚀

To do this we need to add `--dragstr` and `--dragen-mode` : https://gatk.broadinstitute.org/hc/en-us/articles/4407897446939--How-to-Run-germline-single-sample-short-variant-discovery-in-DRAGEN-mode

> I don't suppose the CI-tests of Sentieon will pass: > > [nf-core/modules#4893](https://github.com/nf-core/modules/pull/4893) Server is still down afaik. If @maxulysse agrees would be ok for me to run all tests...

Here are some docs on how to increase resources for specific process without touching the code base: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources

For how to use it, check here: https://nf-co.re/sarek/3.4.0/parameters#tools TL;DR: `--tools ngscheckmate`

Benchmarked this quickly using the Co2 footprint, which is now higher. I will dig more into it to see if this is due to some general fluctuation on the cluster...

Don't see any particular decreases in mem or cpu or work storage. So benefit is avoiding spinning up more machines/reducing number of jobs submitted.

we need more info. Can you please add the .nextflow.log, any custom config files, any parameter files, an overview of the published files, and what files are missing?

Hey! Good news we are working on it @lescai has put in some time to clean this up and fix it :)

or we could rename patient to entity?