Params
The defaults for Cecret correspond with paired-end Illumina sequencing files of amplified SARS-CoV-2 with a specified version of the artic primers. This, however, is not the use-case for everyone, so there are many adjustable parameters/params.
A complete list of all params with their default values can be found in Cecret/nextflow_schema.json
There are many profiles included in the workflow, and they correspond generally with mpox and SARS-CoV-2 sequencing.
The End User should not have to change the files in the Cecret repository in order to get the analyses that they need. Nextflow has a useful option that allows the adjustment of params on the command line.
The general format of adjusting a param on the command line is
nextflow run UPHL-BioNGS/Cecret <what a user would normally run> --<parameter that needs adjusting> "<what it needs to be adjusted to>"
A common use-case with Cecret is for those who want to create a multiple sequence alignment and phylogenetic tree for their samples by adjusting the relatedness param to true.
nextflow run UPHL-BioNGS/Cecret <what a user would normally run> --relatedness true
This works for params that are short and if only one or two need to be adjusted. For longer cases, please read about using config files.
