huddlej

huddlej

custom_rules:
  - profiles/gisaid/prepare_data.smk

metadata_fields:
  - Isolate_Name
  - Isolate_Id
  - Passage_History
  - Location
  - Authors
  - Originating_Lab

huddlej

# Current implementation approach where "subsamples" is defined in build configuration YAML file.
# Build configuration parameters get passed to the optionally-templated subsample "filters" strings
# such that the same subsampling scheme can be shared across multiple builds by passing build-specific
# variables. For the full context of this subsampling scheme, see the original build configuration file:
# https://github.com/nextstrain/seasonal-flu/blob/45bf4336d9485c1c9bfc44b09b384595d7685032/profiles/nextstrain-public.yaml#L78-L86
subsamples: &subsampling-scheme
  regions_except_europe:
    filters: --query "(passage_category != 'egg') & (region != 'Europe') & (ha == True) & (na == True)" --group-by region year month --subsample-max-sequences 2700 --min-date {min_date} --exclude {exclude} --exclude-where passage=egg
    # Note that a priority of "titers" has a special meaning in the flu
    # workflow which is not portable to other pathogen workflows.

huddlej

(Japan/PG-240490/2022:0.00016908,((((((((((((((Ireland/C-Enfer-COV170122075_H10/2022:0.00006838,England/MILK-33EEE7B/2022:0.00006689):0.00000100,((Argentina/INEI118661/2022:0.00013528,(USA/GA-CDC-STM-QN5JEP37F/2022:0.00003344,Slovakia/BA_22_00007824/2022:0.00017280):0.00003344):0.00000100,(Peru/PIU-INS-16129/2022:0.00010259,Brazil/SP-NVBS14337GENOV828793225901/2022:0.00003344):0.00003344):0.00000100):0.00000100,(USA/CA-CDC-ASC210857596/2022:0.00013530,Brazil/GO-2-LACEN-1527/2022:0.00017074):0.00013524):0.00000203,(((((Canada/BC-BCCDC-334228/2022:0.00003344,Peru/ARE-INS-16519/2022:0.00006854):0.00000100,Brazil/RS-FIOCRUZ-10545/2022:0.00023678):0.00003344,Japan/PG-188383/2022:0.00010147):0.00000100,Poland/22SNR578_wsserze/2022:0.00006940):0.00003231,Brazil/CE-FIOCRUZ-79004CE/2022:0.00010111):0.00003344):0.00054049,Wuhan/Hu-1/2019:0.00116797):0.00082379,Belgium/AZDelta-2238-06015/2022:0.00003344):0.00003344,((((((Slovakia/BA_22_00035301/2022:0.00013530,Denmark/DCGC-529344/2022:0.00003344):0.00000100,((Slovenia/5

huddlej

#!/usr/bin/env python3
import argparse
import Bio.Phylo


if __name__ == "__main__":
    parser = argparse.ArgumentParser(
        description="Find polytomies in a given tree",
        formatter_class=argparse.ArgumentDefaultsHelpFormatter
    )

huddlej

huddlej

Example of a composable config for Nextstrain seasonal flu builds using CUE definitions

Background

An example of how one might use a configuration language like CUE to abstract a Nextstrain build configuration across multiple resolutions, segments, or lineages. The attached CUE config defines 20 builds for H3N2 and H1N1pdm lineages, HA and NA segments, and five different resolutions. Resolution- and lineage-specific parameters are defined once as CUE definitions and combined through CUE structs. These 100 lines of CUE (with comments) evaluate to 181 lines of YAML. CUE also allows us to define default values for fields like filter.sequences_per_group that we can override in specific builds. This approach allows us to create builds that require exceptions to the rules like the h3n2_na_6m build.

This example builds on the idea of

huddlej

huddlej

# Define lineages for the analysis.
lineages:
  - h3n2
  - h1n1pdm
  - vic
  - yam

# Define genes to translate from nucleotide to amino acid sequences. These names
# must match coding regions defined in the reference.
genes:

huddlej

Convert Augur node data JSON to data frame format (TSV, CSV, etc.)

This script addresses a use case of how to parse values from Augur's node data JSON files into a data frame format that can be easily consumed by other tools.

The following example shows how to convert a discrete trait analysis output from augur traits in the Nextstrain ncov workflow to a TSV file.

python3 node_data_to_table.py \
  --tree results/europe/tree.nwk \
 --jsons results/europe/traits.json \