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phylogenetic/nextclade: Add links to tutorials and zika/mpox repos #78

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Dec 9, 2024
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phylogenetic/nextclade: Add links to tutorials and zika/mpox repos #78

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phylogenetic/nextclade: Add links to tutorials and zika/mpox repos
joverlee521 Dec 6, 2024
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joverlee521 Dec 9, 2024
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8 changes: 8 additions & 0 deletions nextclade/README.md
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Expand Up @@ -6,6 +6,14 @@ The new standard would be to include the Nextclade workflow within the pathogen
This workflow is used to create the Nextclade datasets for this pathogen.
All official Nextclade datasets are available at https://github.com/nextstrain/nextclade_data.

> [!IMPORTANT]
> We do not have a generalized nextclade workflow so the rules files are empty and
> will need to be filled in with your own rules. We suggest that you go through the
> [Nextclade dataset creation guide](https://github.com/nextstrain/nextclade_data/blob/@/docs/dataset-creation-guide.md)
> to understand how to create a Nextclade dataset from scratch. Then use
> [mpox](https://github.com/nextstrain/mpox) as an example to create your own
> Nextclade workflow.

## Workflow Usage

The workflow can be run from the top level pathogen repo directory:
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8 changes: 8 additions & 0 deletions phylogenetic/README.md
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Expand Up @@ -3,6 +3,14 @@
This workflow uses metadata and sequences to produce one or multiple [Nextstrain datasets][]
that can be visualized in Auspice.

> [!IMPORTANT]
> We do not have a generalized phylogenetic workflow so the rules files are empty and
> will need to be filled in with your own rules. We suggest that you go through the
> ["Creating a phylogenetic workflow" tutorial](https://docs.nextstrain.org/en/latest/tutorials/creating-a-phylogenetic-workflow.html)
> to understand the simplified zika-tutorial workflow. Then use [zika](https://github.com/nextstrain/zika)
> and [mpox](https://github.com/nextstrain/mpox) as examples to create
> your own phylogenetic workflow.

## Workflow Usage

The workflow can be run from the top level pathogen repo directory:
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