subsample: Improve default search paths, allow customization #4046
victorlinci.yaml
on: pull_request
Matrix: pytest-cram
mypy
52s
pyright
20s
build-docs
/
build
1m 35s
check-docs
47s
check-subsample-config-schema
45s
Matrix: pathogen-repo-ci-v0
Matrix: pathogen-repo-ci
codecov
16s
rebuild-docker-image
0s
Annotations
19 warnings
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pyright
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
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check-subsample-config-schema
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
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mypy
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
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pathogen-repo-ci (lassa)
Failed to save: Unable to reserve cache with key 2025-10-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (mumps)
Failed to save: Unable to reserve cache with key 2025-10-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci-v0 (ncov)
Failed to save: Unable to reserve cache with key 2025-10-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (wnv)
Failed to save: Unable to reserve cache with key 2025-10-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci-v0 (avian-flu)
Failed to save: Unable to reserve cache with key 2025-10-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci-v0 (rsv)
Failed to save: Unable to reserve cache with key 2025-10-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci-v0 (vcf-input-tutorial)
Failed to save: Unable to reserve cache with key 2025-10-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (dengue)
Failed to save: Unable to reserve cache with key 2025-10-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (zika)
Failed to save: Unable to reserve cache with key 2025-10-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (mpox)
Failed to save: Unable to reserve cache with key 2025-10-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (measles)
Failed to save: Unable to reserve cache with key 2025-10-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (oropouche)
Failed to save: Unable to reserve cache with key 2025-10-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (seasonal-cov)
Failed to save: Unable to reserve cache with key 2025-10-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (yellow-fever)
Failed to save: Unable to reserve cache with key 2025-10-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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pathogen-repo-ci (rabies)
Failed to save: Unable to reserve cache with key 2025-10-31-linux-64-augur-args-30d39f4-root-dcc80ee-bin-7f980036a54bf9b731e96423dab2167633dab2652673dc4fef598b730ac364cb, another job may be creating this cache.
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codecov
The `python-version` input is not set. The version of Python currently in `PATH` will be used.
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Artifacts
Produced during runtime
| Name | Size | Digest | |
|---|---|---|---|
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coverage
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191 KB |
sha256:a3f06be0300879f734b2b5ef198c04f9bd9ff87f463b9a920e590522eb724e13
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output-avian-flu
|
108 KB |
sha256:728cb52ff0046928866b2f33e58cb95a04832e047dcf2167462cf997e4786258
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output-dengue
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436 KB |
sha256:b731afe4fcdafda9695a02372f591ae1e84c8ce3bd0c49b11a13d569de5cc0dc
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output-lassa
|
369 KB |
sha256:f8f61e4b3f399e4f54495f7a111662aea8e2c376ad57d135d674df6799595c7f
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output-measles
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3.9 MB |
sha256:ae5e35f001527d86acfb3f210450d0bf4651fc570547910c1218e0616c379c33
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output-mpox
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14.4 MB |
sha256:4a2256454e952c038369c7a26bae15565eaba4aa41a2d0601a0cd7c6389caf00
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output-mumps
|
379 KB |
sha256:fadee0324abe8685bb78f9e44bbc904b3651d0877ace1b3368546a5c7eeadbed
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output-ncov
|
716 KB |
sha256:248deecc1ec25c131a6c59b8c50795c316734e41085c22e1e983111c2223e94b
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output-oropouche
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588 KB |
sha256:d91d4b4ebb9fa9efdffd24cc7715f278904154e6645be8b116c80182b9e55a6c
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output-rabies
|
5.28 MB |
sha256:96552ad147826235acc554446706dd492aca737e10e46569e2af25918acd2ce0
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output-rsv
|
1.21 MB |
sha256:5771e3b21f1dd6b04ed062a9ee6b45e5c3bfad46e167aa0cefd4634caf92790d
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output-seasonal-cov
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2.46 MB |
sha256:31b4f9048f5a0bf704536be9870e9a31da1ec37ad0b01367f18675becff4d76f
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output-seasonal-flu
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60.3 KB |
sha256:94f4b37c39f7ee62da2155cf77cb3b13e972f1b984c7f8cd4d6cb98924bf5a0f
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output-vcf-input-tutorial
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5.03 MB |
sha256:ba7e6f4984b753eda03657f8bdcda68dd2ae490817ba14f078314a0e9499ecf4
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output-wnv
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240 KB |
sha256:af952887bcef4875a518271bb4ee3619e7b6ee15ce3d59faed9f4cf30cb81e19
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output-yellow-fever
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2.12 MB |
sha256:15c4e625868208335c3c0ec49d4e593e9abd930acc4c1c6338e695939127efd5
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output-zika
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807 KB |
sha256:076d6cd6d290e84b1d12f08f70bbe26048dc556a5bab7e49a58d1a9e30c82b98
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