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try better empty channel management for germline ressource in mutect2 subworkflow #1309

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merged 3 commits into from
Nov 7, 2023
Merged

try better empty channel management for germline ressource in mutect2 subworkflow #1309

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7d718c1
try better empty channel management
maxulysse Nov 3, 2023
c9d4429
fix typo
maxulysse Nov 3, 2023
bbc71e1
Update subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf
maxulysse Nov 3, 2023
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2 changes: 1 addition & 1 deletion subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf
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Expand Up @@ -31,7 +31,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_MUTECT2 {
versions = Channel.empty()

//If no germline resource is provided, then create an empty channel to avoid GetPileupsummaries from being run
germline_resource_pileup = germline_resource_tbi ? germline_resource : Channel.empty()
germline_resource_pileup = germline_resource_tbi ? germline_resource ?: Channel.empty() : Channel.empty()
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germline_resource_pileup_tbi = germline_resource_tbi ?: Channel.empty()

// Combine input and intervals for spread and gather strategy
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