Hi @Kübra Narcı! I would like to start working on the task Add rtgtools/cnveval #266. I noticed it has been assigned since January and there hasn’t been any recent activity. Would it be okay if I take this task?

Hello, I think it is assigned to @GeorgiaKes, you need her consent :)

Of course! Feel free to work on that!

perfect, than feel free to assign it yourself there, but most importantly here is the issue in nf-core/modules https://github.com/nf-core/modules/issues/10393 start working there

Hi @Kübra Narcı! The module and subworkflow are implemented and working. However, I ran into an issue with test data: cnveval requires truth VCF records wit SVTYPE=DUP or DEL, but the existing truth file (cnv_benchmark_calls.vcf) uses SVTYPE=<CNV:GAIN> and <LOH>, which cnveval doesn't recognize As a workaround, I generated a small truth VCF (assets/test_cnveval_truth.vcf) with 10 DUP/DEL records derived from the existing test data, and the pipeline runs end-to-end successfully with it What would be the preferred approach here? 1. Keep the generated truth VCF locally in assets/ 2. Upload it to nf-core/test-datasets 3. Something else

Hello Sevda, are you creating the module in variantbenchmarking? I think it is best to add the tool to nf-core/modules first as rtgtools/cnveval and then we can pull the tool to variantbenchmarking. inside nf-core/modules/tests there should be more test cases. we prefer not to add tests to assets. If you cannot find a test case in nf-core we can think about another solution 🙂

oh yes, I've done according this instruction ok, I will add it to nf-core/modules first🙂

🙂 yea sorry this instruction is for in general issues for the pipeline, we also like to have tools registred in nf-core/modules to enable common usage (if they met to the criterias..)

Ok, I found instruction for adding a new module to nf-core/modules Thank you for the help!

Hello! thank you very much for the module. you can try to add the tool under subworkflows/local/sv_germline_benchmark/main.nf. This suppose to work

if (params.method.contains('rtgtools') && params.variant_type != "copynumber")

please also add a test case to make sure everything works through