Minimum frequency threshold is being ignored - Githubissues

nf-core / viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

https://nf-co.re/viralrecon

MIT License

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Minimum frequency threshold is being ignored #382

Open AndreaAguadoM opened 1 year ago

AndreaAguadoM commented 1 year ago

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

Relevant files

No response

System information

No response

maxulysse commented 10 months ago

There is no min_allele_freq params. Where did you find reference to this params?