This workflow uses metadata and sequences to produce one or multiple Nextstrain datasets that can be visualized in Auspice.
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.
- 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).
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.
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 ingest Snakefile succinct and
organized. Modules are all included in the main Snakefile in the
order that they are expected to run.