Hello, is there a way to run only the joint calling step? I have done running the haplotypecaller steps, and then the join calling was killed by OOM; however, our cluster has problem with -resume, so it would be nice if I can start with a step of join calling not the whole variant_calling step. Thanks 🙏

no sorry. I have been wanting to implement this for ages: https://github.com/nf-core/sarek/issues/755 but time 😞

🥲, thanks for the response and sharing the git issues!