A tiny change: use a phylogenetic directory #15
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Move phylogenetic workflow from top-level to folder phylogenetic in order to follow the Pathogen Repo Template: https://github.com/nextstrain/pathogen-repo-template
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joverlee521
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Jan 3, 2024
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The majority of the changes look good to me 👍
My only request to is update the CI workflow since it currently does not fully work as intended. Looking at the latest CI job on this branch, there are no artifacts uploaded due to the bug so we cannot inspect the build outputs.
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Reduce confusion of the use of the profiles' config files. They are to be seen as additional profiles' config on top of the default configs. Stems from discussion with @j23414 for review of nextstrain/dengue#15. Note we not using `config.yaml` because this is used by the Snakemake profiles configuration.¹ ¹ https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles
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Hi @joverlee521! This PR is ready for review. Following our earlier discussion, I've implemented further changes, but am open to further revisions.
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Jan 8, 2024
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Jan 8, 2024
| [auspice]: https://docs.nextstrain.org/projects/auspice/en/stable/index.html | ||
| [Installing Nextstrain guide]: https://docs.nextstrain.org/en/latest/install.html | ||
| [Running a Pathogen Workflow guide]: https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html | ||
| - [Contributor documentation](./CONTRIBUTING.md) |
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Just realizing this CONTRIBUTING.md file also does not exist in this repo.
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| Alternatively, you can run the build using the | ||
| example data provided in this repository. Before running the build, copy the | ||
| example sequences into the `data/` directory like so: | ||
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| mkdir -p data/ | ||
| cp example_data/dengue* data/ |
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One other benefit to having the CI profile is users no longer have to manually copy over the example data.
These instructions can be updated to use
nextstrain build . --configfile profiles/ci/profiles_config.yaml
Part of work to update this repo to match the pathogen-repo-template.
Part of work to update this repo to match the pathogen-repo-template.
Part of work to update this repo to match the pathogen-repo-template.
Part of work to update this repo to match the pathogen-repo-template.
Use the stopgap from mpox (nextstrain/mpox#214) until the pathogen-repo-ci is updated.
One benefit to having the CI profile is users no longer have to manually copy over the example data.
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joverlee521
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Reduce confusion of the use of the customizations' config files. They are to be seen as additional custom configs on top of the default configs. Stems from discussion with @j23414 for review of nextstrain/dengue#15.
joverlee521
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Jan 19, 2024
Reduce confusion of the use of the customizations' config files. They are to be seen as additional custom configs on top of the default configs. Stems from discussion with @j23414 for review of nextstrain/dengue#15.
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Description of proposed changes
A tiny change ;) Use a phylogenetic directory to follow the pathogen-repo-template.
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