Marius Bjørnstad

mosdepth is working well on 2.6.0 without override, so this issue is fixed

Seems I have the same problem in NFCORE_RAREDISEASE:RAREDISEASE:CALL_STRUCTURAL_VARIANTS:CALL_SV_TIDDIT:SVDB_MERGE_TIDDIT too

That's a fair point, I'll have a look at how to make it a subworkflow. Already have a prototype for changes to raredisease that I'm testing now https://github.com/fa2k/raredisease/tree/cadd-chrnames

Hi @ramprasadn it's nice that you're looking into this, but the subworkflow solution is proving to be a bit troublesome. DeepVariant made some large changes to the pipeline structure with...

Thanks for the comments - it's a great point about using stageInMode: copy - this would be very inefficient to have many make_examples jobs. And also like you say it...

I've replaced the DEEPVARIANT process with a workflow comprising the three stages. I'm not sure if nf-core allows having a workflow in a module, like that. Here's the current version:...

Yes making a subworkflow seems more aligned with other things in nf-core, and changes are needed in the workflows no matter what. I'm off this week, and will try to...

I've made a draft solution based on splitting the subcommands of DeepVariant into separate modules. These "subcommands" are the commands seen in the log of the run_deepvariant script, used in...

As linked above - I made a new attempt at a pull request, which keeps the existing module as deepvariant/rundeepvariant, and uses the new DeepVariant version (requiring some changes to...