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uclahs-cds / pipeline-call-sSNV

A Nextflow pipeline to identify the somatic single nucleotide variants (sSNVs) by comparing a pair of tumor/normal samples.
https://uclahs-cds.github.io/pipeline-call-sSNV/
GNU General Public License v2.0
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running without a `panel of normals` now elicits a WARNING #308

Closed sorelfitzgibbon closed 1 month ago

sorelfitzgibbon commented 3 months ago

WARN: Access to undefined parameter panel_of_normals_vcf -- Initialise it to a default value eg. `params.panel_of_normals_vcf = some_value

yashpatel6 commented 3 months ago

https://github.com/uclahs-cds/pipeline-call-sSNV/blob/4d5dd5a460073dcb5d9336c154263ec95c4b3c21/module/mutect2-processes.nf#L95

Needs to be updated to

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