Using 8.0.0 as the minimum version because that is when the storage plugins 
were added. Even though we are bumping runtimes to Snakemake v9, we are not 
using any specific v9 features.

This printed the reason for each executed rule but was already
deprecated and always true in v7 [1] and has been removed entirely in
later snakemake versions. The upgrade path is clear [2]: "Deprecated:
Drop it and don't worry about anything"

Note: The same changes were applied to zika [3]

[1] <https://snakemake.readthedocs.io/en/v7.22.0/executing/cli.html#output>
[2] <https://snakemake.readthedocs.io/en/stable/getting_started/migration.html>
[3] <nextstrain/zika#88>

The `--stats` CLI argument is no longer supported and according to
<https://snakemake.readthedocs.io/en/stable/getting_started/migration.html>
there is no suitable replacement. The reports feature looks along the
same lines as stats, but doesn't seem as well suited for our purposes.
See <#1180 (comment)>
for more discussion around this.

The keyword storage now has a special meaning in Snakemake
<https://snakemake.readthedocs.io/en/stable/snakefiles/storage.html>.
Rename our existing usage of this variable to avoid conflicts.

As we now require snakemake v8 we can leverage the more convenient
`input.size_mb` functionality, which is functionally equivalent to
`input.size / 1024 / 1024` [1]

The `rule colors` wants the size of an individual input (not the sum of
all inputs) and the `_IOFile.size` function is now a coroutine. The more
widely used (by us) `InputFiles.size` function uses `async_run` to allow
coroutine calls so I think it's fine for us to do so explicitly to get
the size of an individual file. Other code paths end up at the same
point, such as `input.size_files_mb[list(input.keys()).index('metadata')]`

Closes #1114

[1] <https://github.com/snakemake/snakemake/blob/7f2606e453ba6bd83222ec3679178ae96bd142d2/src/snakemake/io/__init__.py#L1894-L1923>
[2] <https://github.com/snakemake/snakemake/blob/7f2606e453ba6bd83222ec3679178ae96bd142d2/src/snakemake/io/__init__.py#L622-L633>

With Snakemake v9 we observed the following error:

    No validator found for JSON Schema version identifier 'http://json-schema.org/draft-06/schema'
    Defaulting to validator for JSON Schema version 'https://json-schema.org/draft/2020-12/schema'
    Note that schema file may not be validated correctly.

There's nothing salient in
<https://snakemake.readthedocs.io/en/stable/project_info/history.html>
indicating why this happened but it wasn't observed in v7. I read
through the migration guides to get us up to 2020-12
<https://json-schema.org/specification/migration> and didn't find any
changed needed, which matches with the validation of our schema using
the new schema defs.

If we wish to support this again in the future we can re-implement it
in a snakemake v9 compatible way. Given the hardcoded paths in the
config I'm confident this was only ever used by the neher lab and not
external users.