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running without a panel of normals now elicits a WARNING #308

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sorelfitzgibbon opened this issue Aug 17, 2024 · 1 comment · Fixed by #319
Closed

running without a panel of normals now elicits a WARNING #308

sorelfitzgibbon opened this issue Aug 17, 2024 · 1 comment · Fixed by #319

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@sorelfitzgibbon
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WARN: Access to undefined parameter panel_of_normals_vcf -- Initialise it to a default value eg. `params.panel_of_normals_vcf = some_value
@yashpatel6
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pipeline-call-sSNV/module/mutect2-processes.nf

Line 95 in 4d5dd5a

panel_of_normals = params.panel_of_normals_vcf ? "--panel-of-normals ${params.panel_of_normals_vcf}" : ""

Needs to be updated to

panel_of_normals =  params.getOrDefault("panel_of_normals_vcf", null) ? "--panel-of-normals ${params.panel_of_normals_vcf}" : ""

@sorelfitzgibbon sorelfitzgibbon mentioned this issue Oct 25, 2024
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fix check for panel of normals and add in log uclahs-cds/pipeline-call-sSNV
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@sorelfitzgibbon @yashpatel6