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Phylogenetic

This workflow uses metadata and sequences to produce one or multiple Nextstrain datasets that can be visualized in Auspice.

Workflow Usage

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

nextstrain build phylogenetic

Alternatively, the workflow can also be run from within the phylogenetic directory:

cd phylogenetic
nextstrain build .

This produces the default outputs of the phylogenetic workflow:

  • auspice_json(s) = auspice/*.json

Data Requirements

The core phylogenetic workflow will use metadata values as-is, so please do any desired data formatting and curations as part of the ingest workflow.

  1. The metadata must include an ID column that can be used as as exact match for the sequence ID present in the FASTA headers.
  2. The date column in the metadata must be in ISO 8601 date format (i.e. YYYY-MM-DD).
  3. Ambiguous dates should be masked with XX (e.g. 2023-01-XX).

Defaults

The defaults directory contains all of the default configurations for the phylogenetic workflow.

defaults/config.yaml contains all of the default configuration parameters used for the phylogenetic workflow. Use Snakemake's --configfile/--config options to override these default values.

Snakefile and rules

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.

Build configs

The build-configs directory contains custom configs and rules that override and/or extend the default workflow.

  • ci - CI build that runs with example data