This workflow uses metadata and sequences to produce one or multiple Nextstrain datasets that can be visualized in Auspice.
There are currently two separate workflows:
- The outbreak-specific workflow (entrypoint:
./outbreak-specific/Snakefile) which generates analyses for individual outbreaks - The all-outbreaks workflow (entrypoint:
./all-outbreaks/Snakefile)
Currently the workflows use starting data from a local ingest run, so there must be files in
../ingest/results/
This workflow produces a single analysis of the West Africa outbreak.
The workflow can be run from the top level pathogen repo directory:
nextstrain build phylogenetic --snakefile outbreak-specific/Snakefile
The resulting dataset can be viewed in a web browser:
nextstrain view phylogenetic/outbreak-specific
This workflow subsamples genomes across outbreaks to present an overview of the known genomic history of Ebola virus (EBOV), formerly Zaïre ebolavirus. Outbreaks are classified using Nextclade as part of the ingest workflow. The rooting of the tree is chosen to match McCrone et al., Virological (2025) and the phylogeny is currently divergence-only.
The workflow can be run from the top level pathogen repo directory:
nextstrain build phylogenetic --snakefile all-outbreaks/Snakefile
The resulting dataset can be viewed in a web browser:
nextstrain view phylogenetic
Input data
By default the workflow requires locally ingested data.
You can our canonical data from s3 by adding --config s3=True to your command.
Note
The local & S3 data sources currently include restricted PPX data. If you are sharing these analyses you must ensure you abide by Pathoplexus' Restricted Data Terms of Use
The phylogenetic workflows will use metadata values as-is, so please do any desired data formatting and curations as part of the ingest workflow.
- The metadata must include an ID column that can be used as as exact match for the sequence ID present in the FASTA headers.
- The
datecolumn in the metadata must be in ISO 8601 date format (i.e. YYYY-MM-DD). - Ambiguous dates should be masked with
XX(e.g. 2023-01-XX).
Note
This section only applies to the outbreak-specific workflow and not the all-outbreaks workflow.
The rules directory contains separate Snakefiles (*.smk) as modules of the core phylogenetic workflow.
The modules of the workflow are in separate files to keep the main phylogenetic Snakefile succinct and organized.
The workdir is hardcoded to be the phylogenetic directory so all filepaths for
inputs/outputs should be relative to the phylogenetic directory.
Modules are all included in the main Snakefile in the order that they are expected to run.
The build-configs directory contains custom configs and rules that override and/or extend the default workflows.
- ci - CI build that runs with example data