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Minimum frequency threshold is being ignored #382

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AndreaAguadoM opened this issue Jun 6, 2023 · 1 comment
Open

Minimum frequency threshold is being ignored #382

AndreaAguadoM opened this issue Jun 6, 2023 · 1 comment
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@AndreaAguadoM
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Description of the bug

Hello.
I am trying to use viralrecon as to detect variants with a minimun frequency of 0.1. Nevertheless, when using viralrecon with the instructions given below, I have found the following warning:

WARN: Found unexpected parameters:

  • --min_allele_freq: 0.1

the min_allele_freq is being ignored. What can I do?

Thanks in advance!

Command used and terminal output

$ nextflow run nf-core/viralrecon --input samplesheet.csv --genome 'MN908947.3' --min_allele_freq 0.1 -profile singularity --primer_bed nCoV-2019.artic.V4_1.bed --outdir viralrecon_output/ --platform illumina --protocol amplicon

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@AndreaAguadoM AndreaAguadoM added the bug Something isn't working label Jun 6, 2023
@maxulysse
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There is no min_allele_freq params.
Where did you find reference to this params?

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