mpox
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nextstrain
Nextstrain build for mpox virus
The `hmpxv1_big` build [failed yesterday](https://bedfordlab.slack.com/archives/C03J4JG4ZE0/p1705867758402819) with a validation error from `augur export v2` ``` [batch] [2024-01-21T16:43:57-08:00] Validating schema of 'results/hmpxv1_big/nt_muts.json'... [batch] [2024-01-21T16:43:57-08:00] Validating schema of 'results/hmpxv1_big/aa_muts.json'... [batch] [2024-01-21T16:43:57-08:00] Validating config...
## Context Sometimes running the phylo workflow with the CI configs locally includes the `update_example_data` rule in the DAG: ``` $ nextstrain build . --configfile profiles/ci/builds.yaml -n Building DAG of...
Right now we seem to exclude sequences from the B.1 build that lack a month, i.e. year-only sequences 2022-XX-XX They get filtered out in subsampling as they don't find neatly...
## Description of proposed changes Draft of an attempt to eradicate confounding of "release" and "submission". Inspired by comment: * https://github.com/nextstrain/dengue/pull/13#discussion_r1373356935 Still need to trace through `phylogenetic` rules and scripts...
(Originally flagged the obsolete `reverse` column in https://github.com/nextstrain/monkeypox/pull/207#discussion_r1349164763) Reverse complement sequences were initially manually flagged by the `reverse` column added in https://github.com/nextstrain/monkeypox/pull/79. Since [Nextclade v2.2.0](https://github.com/nextstrain/nextclade/releases/tag/2.2.0), there's a built-in `--retry-reverse-complement` option...
The `reverse` column has effectively been replaced by `is_reverse_complement` from the Nextclade output. The script `ingest/bin/reverse_reversed_sequences.py` is no longer used because it's function is now built into Nextclade. Resolves https://github.com/nextstrain/monkeypox/issues/209....
### Context Thought I take notes on what needs to be taken into account when moving a workflow to a folder. These are all the relevant commits I could find...
Right now we seem to label sequences as reverse-complemented in ingest, but we don't actually fix the wrong orientation in the output sequences. It would make downstream processing easier if...
EPI_ISL_15293815 It's an imported case from Chongqing. EPI_ISL_17809521 It seems to be monkeypox from Hangzhou?
### Context This feature request aims to enhance the understanding of monkeypox epidemiology and transmission patterns. ### Description Currently, in the ncov build of Nextstrain, when running the pipeline locally,...
