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Rename monkeypox -> mpox (virus) when not affecting code #169

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Aug 10, 2023
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Rename monkeypox -> mpox (virus) when not affecting code #169

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2 changes: 1 addition & 1 deletion README.md
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# nextstrain.org/monkeypox

This is the [Nextstrain](https://nextstrain.org) build for MPXV (monkeypox virus). Output from this build is visible at [nextstrain.org/monkeypox](https://nextstrain.org/monkeypox).
This is the [Nextstrain](https://nextstrain.org) build for MPXV (mpox virus). Output from this build is visible at [nextstrain.org/monkeypox](https://nextstrain.org/monkeypox).
The lineages within the recent mpox outbreaks in humans are defined in a separate [lineage-designation repository](https://github.com/mpxv-lineages/lineage-designation).

## Usage
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2 changes: 1 addition & 1 deletion ingest/README.md
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# nextstrain.org/monkeypox/ingest

This is the ingest pipeline for Monkeypox virus sequences.
This is the ingest pipeline for mpox virus sequences.

## Usage

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2 changes: 1 addition & 1 deletion ingest/bin/genbank-url
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#!/usr/bin/env python3
"""
Generate URL to download all Monkeypox sequences and their curated metadata
Generate URL to download all mpox virus sequences and their curated metadata
from GenBank via NCBI Virus.

The URL this program builds is based on the URL for SARS-CoV-2 constructed with
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2 changes: 1 addition & 1 deletion ingest/config/config.yaml
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Expand Up @@ -37,7 +37,7 @@ transform:
abbr_authors_field: 'abbr_authors'
# General geolocation rules to apply to geolocation fields
geolocation_rules_url: 'https://raw.githubusercontent.com/nextstrain/ncov-ingest/master/source-data/gisaid_geoLocationRules.tsv'
# Local geolocation rules that are only applicable to monkeypox data
# Local geolocation rules that are only applicable to mpox data
# Local rules can overwrite the general geolocation rules provided above
local_geolocation_rules: 'source-data/geolocation-rules.tsv'
# User annotations file
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