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Make Markdown output for reports #129

Merged
merged 6 commits into from
Nov 27, 2023
Merged

Make Markdown output for reports #129

merged 6 commits into from
Nov 27, 2023

Commits on Nov 27, 2023

  1. Make Markdown tables about derived haplotypes for narratives

    @huddlej
    huddlej committed Nov 27, 2023
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  2. Add script and rule to generate counts per clade for reports

    @huddlej
    huddlej committed Nov 27, 2023
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  3. Update nextflu-private instructions to include counts by clade

    @huddlej
    huddlej committed Nov 27, 2023
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  4. Count tips by subclade

    @huddlej
    huddlej committed Nov 27, 2023
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  5. Use tabulate's float formatting for tables 

    Instead of rounding decimal values prior creation of the Markdown table
output, use tabulate's own `floatfmt` argument to control that display
detail. Since we used to round current frequencies to 2 decimals and
then filter haplotypes with frequency of zero, we now filter for
haplotypes with a current frequency of at least 1% which produces the
same effect but in a clearer way.
    @huddlej
    huddlej committed Nov 27, 2023
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  6. Bump augur and tabulate versions to latest

    @huddlej
    huddlej committed Nov 27, 2023
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