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nf-core / raredisease

Call and score variants from WGS/WES of rare disease patients.

Home Page:https://nf-co.re/raredisease

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GATK4_GERMLINECNVCALLER modules don't emit .calls. Should be .cohortcalls or .casecalls?

bnjvrjnke opened this issue · comments

commented

call_sv_germlinecnvcaller.nf use GATK4_GERMLINECNVCALLER.out.calls

raredisease/subworkflows/local/variant_calling/call_sv_germlinecnvcaller.nf

Line 43 in 752a9e1

GATK4_GERMLINECNVCALLER.out.calls.toList()

GATK4_GERMLINECNVCALLER module only emit cohortcalls and casecalls

raredisease/modules/nf-core/gatk4/germlinecnvcaller/main.nf

Line 12 in 752a9e1

tuple val(meta), path("*-cnv-model/*-calls"), emit: cohortcalls, optional: true

commented

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

commented

This is now fixed in the latest release @bnjvrjnke.