How to assemble data without providing '--fasta genome.fa'

[nitinShukla1912]

I am trying to assemble illumina viral reads using spades, for a different virus

nextflow run nf-core/viralrecon -profile docker --input samplesheet.csv --platform illumina --outdir nf-Sample1 --protocol metagenomic --skip_nextclade --assemblers 'spades'

Everytime it is asking me to provide '--fasta genome.fa' is it compulsory?

[Joon-Klaps]

Hi,

You can run only the assemblers using the argument --skip_variants it won't ask then for a --fasta. For more info have a look at our docs.