search

nextstrain / seasonal-flu

Scripts. config, and snakefiles for seasonal-flu nextstrain builds
44 stars 26 forks source link

Make Markdown output for reports #129

Closed huddlej closed 9 months ago

huddlej commented 9 months ago

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.

Checklist

huddlej commented 9 months ago

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.