sarscov2‐wastewater
This workflow has also been used with primer-amplified Illumina sequencing of wastewater. Patient samples conceptually are different than wastewater samples, but many of the bioinformatic steps are the same. The files from Freyja are likely the most significant for this analysis. Freyja uses the bam files after primer trimming has been completed to look for variants and their proportions to assign expected pangolin lineages.
Recommended parameter adjustements for wastewater
params.species = 'sarscov2' //this is the default, but it is required for the subworkflow that involves freyja
params.bcftools_variants = false
params.ivar_variants = false
params.pangolin = false
params.nextclade = false
params.vadr = false
Pangolin, Nextclade, and any analysis that evaluates the consensus fasta are not as useful in the context of wastewater. There is currently not a way to remove consensus sequence generation from Cecret, but an option may be available in the future if there is "enough" demand.
