The defaults for Cecret continue to be for SARS-CoV-2, but there are growing demands for a workflow for Monkeypox Virus. As such, there are a few parameters that might benefit the End User.

There are three profiles for Monkeypox Virus sequencing : mpx, mpx_idt and mpx_primalseq. The mpx profile has some defaults for a metagenomic-type sequencing, while mpx_idt is for libraries prepped with IDT's primers, and mpx_primalseq which has been validated with Illumina library prep methods and sequencing platforms.

# metagenomic
nextflow run UPHL-BioNGS/Cecret -profile singularity,mpx

# using IDT's primers
nextflow run UPHL-BioNGS/Cecret -profile singularity,mpx_idt

# using Illumina library prep methods and sequencing platforms
nextflow run UPHL-BioNGS/Cecret -profile singularity,mpx_primalseq