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## Context
Our automated workflows use short lived AWS credentials for sessions which are limited by the [max_session_duration](https://github.com/nextstrain/infra/blob/814a7e4cd635b40c12fb0c4e83b168…
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We've had a history of caching issues (https://github.com/nextstrain/ncov-ingest/issues/456, https://github.com/nextstrain/ncov-ingest/issues/392) come up whenever there's a new release of Nextclade o…
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Prompted by discussion in [blab/forecasting project](https://docs.google.com/document/d/1uioKPOF1U34EiheboX6UVe6pCnfRkdZouUXjgQLLLa4/edit#heading=h.b6uq0bfygq0t)
Naively, we could include the Nextc…
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Implement a branch with nf-ncov-voc using singularity instead of conda
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**Disclaimer: this discussion is limited within scientific community**
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Allow users to select between conda, singularity, etc. for nf-ncov-voc
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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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We've seen an error in `format_pileup.py` where a `KeyError` can be triggered here:
https://github.com/jts/ncov-tools/blob/7a19778c644594fe17ce4fc703560e97b149aa60/workflow/scripts/format_pileup.py…
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### Description of the bug
It is my first time running nf-core/viralrecon pipeline using a sequence from nanopore (Minion). I used the following script but th Pipeline completed with errors. Is the…
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Prompted by https://github.com/nextstrain/ncov-ingest/issues/446
Some ideas of speeding up `upload-to-s3` proposed in related [Slack thread](https://bedfordlab.slack.com/archives/C01LCTT7JNN/p1718…