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[cattle-flu] consistent colours #102

Merged
merged 5 commits into from
Nov 4, 2024
Merged

[cattle-flu] consistent colours #102

merged 5 commits into from
Nov 4, 2024

Commits on Oct 31, 2024

  1. Use per-build metadata files 

    The previous implementation generated a metadata file for each subtype
(i.e. before filtering) and then used that for all downstream rules.
It's more common to (also) generate a post-subsampling metadata file
and use this instead. This is both smaller and useful for debugging
(as all the data in the TSV file are used in the build). It's also
going to make generating colours for specific builds much easier,
which I'll do in subsequent commits.
    @jameshadfield
    jameshadfield committed Oct 31, 2024
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  2. Simplify metadata modifications 

    This shifts the modification of metadata which is specific to the
h5n1-cattle-outbreak/genome/default build to be downstream of the
subsetted-metadata file, which is much simpler to reason with.

We could consider doing something similar for the `add_h5_clade` rule,
however this wouldn't allow us to use that data as a filtering criteria,
and it seems plausible we'd want to do that one day.
    @jameshadfield
    jameshadfield committed Oct 31, 2024
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  3. rearrange snakefiles 

    Make variables and functions defined in the snakefile available to
custom rule files such as cattle-flu.smk. See
<#100 (comment)>
for more context.
    @jameshadfield
    jameshadfield committed Oct 31, 2024
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  4. Consistent coloring for genome builds 

    Uses our well-established pattern of a color-ordering file and a set of
hexes to produce a well-ordered color pallet. Here we restrict the
values within the generating script to better maximise the final
color range (rather than setting colors for all divisions then having
augur export subset them). This approach also ensures colors are
consistent across "division" and "division_metadata" which aids
interpretation of the data.

Closes #101
    @jameshadfield
    jameshadfield committed Oct 31, 2024
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  5. [cattle-flu] consistent colours across segments 

    It's possible segment-level builds will include a division not found
in the genome build, but in this case Auspice will use a grey colour
swatch which I think is acceptable.
    @jameshadfield
    jameshadfield committed Oct 31, 2024
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