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We had a question Nextstrain office hours where a user was running into an error with the curate rule in the ingest workflow:
```
/usr/bin/env: ‘python3\r’: No such file or directory
```
@gene…
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In the line chart, it doesn't make sense to have "Unknown":
For the other plots and for t…
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See #84 for context, follow up on #89
Update pathogen repos to use the latest version of the `pathogen-repo-ci`. We can start with the pathogens that have already been "modernized". Other pathogen …
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I spotted a strange bug on the wnv preview deployment. The organism selector is missing one organism, but only on the review page:
On closer look, it could be that it is a z-index thing, where th…
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Repro: https://lapis-main.loculus.org/mpox/sample/unalignedNucleotideSequences?versionStatus=LATEST_VERSION (only works if there are no sequences on an instance, like right now)
```json
{
"…
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Best practice is to use the Date_report for date_confirmation/death when not explicitly reported by source. This is what we have done for mpox and other outbreaks.
Does our best practice fit Case …
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Both locally and on main, I am observing that for the dummy organism, there is a processing pipeline running with version 2 but for ebola and mpox, there is only a pipeline with version 1. That means …
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https://github.com/theiagen/public_health_bioinformatics/blob/092f19a0f610eb0a01757456932519bbbfe2bbd9/workflows/utilities/wf_organism_parameters.wdl#L254
I tried running a sample with `organism` s…
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**Description**
Numbering of amino acids in output of ivar variants doesn't account for strand and therefore returns incorrect numbering for genes on - strand.
**Command to reproduce behavior**
…
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Prompted by https://github.com/nextstrain/ncov-ingest/issues/456#issuecomment-2218083580
From my reading of [Snakemake docs on threads](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.h…