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nextstrain
The Nextstrain command-line interface (CLI)—a program called nextstrain—which aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Ausp...
Support `nextstrain run` for unmanaged pathogen sources, i.e. working copies of our repos, to aid development. Two avenues to consider for such support. 1. "Editable" setups: `nextstrain setup` pointed at...
## Description of proposed changes Report failures for all jobs but `write-install-commands`, which is more of an intermediate helper than something to report errors for. If this gets noisy for...
_from https://github.com/nextstrain/cli/issues/411#issuecomment-2644073326_ Similar to https://github.com/nextstrain/conda-base/issues/84 but for the scheduled CI in this repo.
Conditions on the Nextstrain CLI version being requested, as aarch64 builds¹ will only be available going forward for new releases. Assumes the next release will be 10.4.2! We must wait...
GitHub released public runners.¹ This will ultimately let us use standalone installation archives in our linux/arm64 Docker images.² Changes to the standalone installer to follow separately³, as those need to...
## Description of proposed changes Allow maintainers to define paths to each workflow's Snakefile and configfile in the nextstrain-pathogen.yaml. Using mpox as an example, this allows the named workflows to...
_continuing discussions from https://github.com/nextstrain/cli/issues/444#issuecomment-3020819959_ Better support `nextstrain setup` and `nextstrain run` for third-party repositories, including private ones. Two avenues to consider for such support. 1. Indirectly with [local support](https://github.com/nextstrain/cli/issues/420), i.e....
This is in early stages, so preliminary discussions are in an [internal Google doc](https://docs.google.com/document/d/1KrElHFEk8c-2zHDs91OqZU0AKme_7WBJ6REUbEzk6aU/edit?usp=sharing).
Context on [Slack](https://bedfordlab.slack.com/archives/C0K3GS3J8/p1750102004221449). If a user runs an AWS Batch job with a short-lived AWS SSO session token then their job must complete within the session duration. In cases where...
Prompted by https://github.com/nextstrain/docs.nextstrain.org/pull/210#issuecomment-3243211810, I was reading Snakemake [docs on benchmarks](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#benchmark-rules) and realized there's a new `--benchmark-extended` flag > Since version 8.11.0, it is possible to have extra benchmark metrics with...
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The Nextstrain command-line interface (CLI)—a program called nextstrain—which aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Ausp...