8000 GATK4_GERMLINECNVCALLER modules don't emit .calls. Should be .cohortcalls or .casecalls? · Issue #535 · nf-core/raredisease · GitHub
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GATK4_GERMLINECNVCALLER modules don't emit .calls. Should be .cohortcalls or .casecalls? #535

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bnjvrjnke opened this issue Mar 21, 2024 · 2 comments
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GATK4_GERMLINECNVCALLER modules don't emit .calls. Should be .cohortcalls or .casecalls? #535

bnjvrjnke opened this issue Mar 21, 2024 · 2 comments
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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

@bnjvrjnke bnjvrjnke changed the title GATK4_GERMLINECNVCALLER modules don't emit .calls. Should be cohortcalls or casecalls? GATK4_GERMLINECNVCALLER modules don't emit .calls. Should be .cohortcalls or .casecalls? Mar 21, 2024
@jemten jemten added the bug Something isn't working label Mar 21, 2024
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jemten commented Mar 21, 2024

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

@ramprasadn ramprasadn mentioned this issue Mar 25, 2024
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This is now fixed in the latest release @bnjvrjnke.

@jemten jemten closed this as completed Apr 2, 2024
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