Workflow Updates

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