Make Markdown output for reports #129
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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.
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These changes only affect the nextflu-private builds, so I'm going to merge this now, and we can use it in our next monthly report in December and continue to build on this functionality in our efforts to automate more parts of these reports. |
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Description of proposed changes
Adds Snakemake rules and scripts to make Markdown tables as part of the nextflu-private workflow, so we can add these tables to our monthly reports.
Related issue(s)
The functionality from this PR depends on the tabulate package. This package gets installed implicitly in Nextstrain Docker and Conda runtimes as a dependency of Snakemake, however we will want to eventually install tabulate in those runtimes explicitly to document that we depend on it directly. See this Slack thread for more details.
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