Add CI profile to run CI build #214
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joverlee521
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tsibley
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joverlee521
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| run: | | ||
| nextstrain build \ | ||
| phylogenetic \ | ||
| --configfile profiles/ci/builds.yaml |
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I realized today that we don't need the CI profile since we can copy over the example data here:
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| run: | | |
| nextstrain build \ | |
| phylogenetic \ | |
| --configfile profiles/ci/builds.yaml | |
| run: | | |
| mkdir -p phylogenetic/data; | |
| cp -r -v phylogenetic/example_data/* phylogenetic/data/; | |
| nextstrain build phylogenetic |
However, it's still nice to be able to run the example build with the single nextstrain build command, so I'm keeping it.
Implements the same method used in ncov¹ and seasonal-flu² for allowing users to add custom rules to the Snakemake workflow. This will be used in subsequent commits to add custom rules for Nextstrain CI workflow that are not required to run the core ingest workflow. ¹ https://github.com/nextstrain/ncov/blob/a29a3b2d98b0835444a88c819925fae07ac9b826/Snakefile#L175-L177 ² https://github.com/nextstrain/seasonal-flu/blob/06865c26a2d972252fde15735d001eaec261126f/Snakefile#L40-L42
Adds custom rule to copy over the example data to be able to run the build with example data. This allows users to run the example build without having to manually copy over the data.
Since the `pathogen-repo-ci` workflow does not allow for custom build directories, use the `pathogen-repo-build` workflow instead.
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Merging to fix the CI since it's been broken due to rebasing in nextstrain/.github#62. |
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j23414
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Jan 5, 2024
Use the stopgap from mpox (nextstrain/mpox#214) until the pathogen-repo-ci is updated.
j23414
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Use the stopgap from mpox (nextstrain/mpox#214) until the pathogen-repo-ci is updated.
j23414
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Use the stopgap from mpox (nextstrain/mpox#214) until the pathogen-repo-ci is updated. However, we may be moving to using config/customization/ci in the future, so revisit this commit and edit accordingly. nextstrain/pathogen-repo-guide#24
j23414
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Use the stopgap from mpox (nextstrain/mpox#214) until the pathogen-repo-ci is updated. However, we may be moving to using config/customization/ci in the future, so revisit this commit and edit accordingly. nextstrain/pathogen-repo-guide#24
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Description of proposed changes
This is an alternative to nextstrain/.github#62, where we migrate the CI job to use pathogen-repo-build workflow instead of the pathogen-repo-ci workflow.
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