Cecret Updates:
* process ivar_variants and ivar_consensus have memory designations so that it doesn't fail as often
* process samtools_plot_ampliconstats has been added
* process vadr has been added
* process bedtools has been renamed to bedtools_multicov and now requires the user to supply the amplicon file (instead of me trying to imagine what it would be from the primer bedfile)
* ivar variants now creates a pseudo vcf file for bamsnap.
* `--annotation` has been added an option, just in case the end user wants to run pangolin, nextclade, vadr, mafft/snpdists/iqtree on a collection of fastas
* process filter has been added
* most processes now have a free text `*_options` parameter to make it easier for the end user to modify options
* `container` and `stageInMode` have been added to processes in the main file
* renaming files now has an external as opposed to internal script
* I've adjusted the config file template into something that makes more sense to me and added more variables
Monroe ONT Updates
* Removed Nanopolish option
* Updated ARTIC workflow and added Medaka models
* Option to use reads that are already basecalled and de-multiplexed