Minimum frequency threshold is being ignored

[AndreaAguadoM]

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]

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

[TKMarkCheng]

I think this is in reference to --min-allele_freq in ivar_variants_to_vcf.py

viralrecon/bin/ivar_variants_to_vcf.py

Line 32 in 3731dd3

"--allele_freq_threshold",

Which is a post-processing step downstream of ivar_variants.

nextflow.config itself actually doesn't take such an argument. In modules_illumina.config, the threshold is fixed at 0.25, which is likely the issue.

viralrecon/conf/modules_illumina.config

Lines 356 to 357 in 3731dd3

	withName: 'IVAR_VARIANTS' {
	ext.args = '-t 0.25 -q 20 -m 10'