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Update nextflu-private instructions
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Simplify instructions for private builds to reflect that more report
contents get automatically generated now.
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huddlej committed May 13, 2024
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30 changes: 8 additions & 22 deletions profiles/nextflu-private/README.md
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Expand Up @@ -26,29 +26,15 @@ nextstrain remote upload \
narratives/nextstrain-cdc_2022-10-03.md
```

## Update the group overview

[The nextflu-private group's overview](https://nextstrain.org/groups/nextflu-private/) lists recent reports and trees by date with the most recent at the top of the page.
[Open the group's settings page](https://nextstrain.org/groups/nextflu-private/settings) and update the list of builds to include the builds you just uploaded.
The nextflu-private workflow automatically generates several outputs used for reporting including:

## Plot counts per lineage for reports
- Plots of the number of genomes available in GISAID for all lineages (e.g., `figures/total-sample-count-by-lineage.png`)
- Markdown tables of counts of samples collected in the last month per build and clade (e.g., `builds/h1n1pdm_2y_titers/counts_of_recent_tips_by_clade.md`)
- Markdown tables of current frequency, change in frequency in the last 4 weeks, and titer reference strains for derived haplotypes (e.g., `builds/h1n1pdm_2y_titers/ha/haplotype_summary/cell_hi.md` per titer collection)

Plot the number of genomes available in GISAID for all lineages in a single plot and then plot number per region within each lineage.
Plots use Altair which is not part of the Nextstrain Docker or Conda base environments, so we use a custom Conda environment with Snakemake.
Copy these files (or their contents) into the corresponding sections of the narrative Markdown.

``` bash
snakemake \
figures/total-sample-count-by-lineage.png \
--use-conda \
--conda-frontend conda \
-j 1 \
-p \
--configfile profiles/nextflu-private.yaml
```

The private builds also produce Markdown table summarizing two different types of lineage or genotype counts:

- counts of samples collected in the last month per build and clade (e.g., `builds/h1n1pdm_2y_titers/counts_of_recent_tips_by_clade.md`)
- current frequency, change in frequency in the last 4 weeks, and titer reference strains for derived haplotypes (e.g., `builds/h1n1pdm_2y_titers/ha/haplotype_summary/cell_hi.md` per titer collection)
## Update the group overview

Copy the contents of these files into the corresponding sections of the narrative Markdown.
[The nextflu-private group's overview](https://nextstrain.org/groups/nextflu-private/) lists recent reports and trees by date with the most recent at the top of the page.
[Open the group's settings page](https://nextstrain.org/groups/nextflu-private/settings) and update the list of builds to include the builds you just uploaded.

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