This is to bring Cecret up-to-date in a couple of areas
There is now a nextflow_schema.json file that should make Cecret compatible with the staphb toolkit (again)
There are now some defaults for monkeypox.
Warning : this is assuming that the monkeypox reads were generated without any sort of bait or amplicon approach. This workflow will need to be amended if a different library prep technique becomes the norm.
As there are now monkeypox and sars-cov-2 defaults, a new parameter, species, has been introduced with several corresponding parameter changes. There is also a mpx and sarscov2 profile, which are highly recommended
This is to bring Cecret up-to-date in a couple of areas
Warning : this is assuming that the monkeypox reads were generated without any sort of bait or amplicon approach. This workflow will need to be amended if a different library prep technique becomes the norm.