future_improvements

- preprocess_cog_uk takes a file of updated dates: could this be fed back into majora so
no longer needed?
- omissions file: is it really necessary still?
- what is best practice: add lots of inputs, or have global params used by processes and minimal inputs?
- in general, fix inputs/params so cast as a file/path at the right point allowing no file in some cases
- what should desired result be if missing input files e.g. list of aas/dels to search for and add to metadata table.
Set up now to skip that step
- Lots of very similar looking python scripts within processes - these were fastafunks, but were replaced
to speed up. Could instead speed up fastafunk in the same way.
- Used to retain info week to week about which samples were eliminated as duplicates - this is now done denovo each
week which is probably desirable behaviour?
- Used to have min length and min covg thresholds, now have just one lower min_covg threshold because if not tree
building don't need higher covg?
- Changes from before: when publishing use recipes
    - remove mutations from consortium metadata, add them to variants metadata
    - remove phylogenetics columns, make phylogenetics metadata later
- might want to publish developer info to a directory e.g. geography outputs inc new dodgy stuff
- command line help and specify required arguments
- containerize and get rid of conda environment - can be parsed down at the same time as includes things from other
steps of the old pipeline
- add back in resource requirements