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nf-core / raredisease

Call and score variants from WGS/WES of rare disease patients.
https://nf-co.re/raredisease
MIT License
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GATK4_GERMLINECNVCALLER modules don't emit .calls. Should be .cohortcalls or .casecalls? #535

Closed bnjvrjnke closed 6 months ago

bnjvrjnke commented 6 months ago

call_sv_germlinecnvcaller.nf use GATK4_GERMLINECNVCALLER.out.calls https://github.com/nf-core/raredisease/blob/752a9e172d710c8c67bbb6791955c91eb6f5fbde/subworkflows/local/variant_calling/call_sv_germlinecnvcaller.nf#L43

GATK4_GERMLINECNVCALLER module only emit cohortcalls and casecalls https://github.com/nf-core/raredisease/blob/752a9e172d710c8c67bbb6791955c91eb6f5fbde/modules/nf-core/gatk4/germlinecnvcaller/main.nf#L12

jemten commented 6 months ago

Thanks for reporting @bnjvrjnke. We'll make a patch for this

ramprasadn commented 6 months ago

This is now fixed in the latest release @bnjvrjnke.