Hi, I've been running the pipeline using a sample sheet that contains multiple

case_id

values, but I’ve noticed that the output always generates a single

<case_id>_snv.vcf.gz

file, named after the first

case_id

in the list. I'm wondering is this the expected behavior? Should the pipeline produce one VCF per

case_id

, or am I possibly missing something in how the sample sheet or parameters are configured?

Hi @Blaž Vrhovšek! The current version of the pipeline can only handle one case at a time. I thought we had a check to prevent users from including multiple case IDs in a single samplesheet, but it seems I missed that. Sorry about that. There was a request from another user as well to add this feature for handling multiple cases, but it likely won't be implemented before summer. Could you create an issue on github?