Add ingest #6
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Add ingest #6
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Copy the ingest directory from pathogen-repo-guide https://github.com/nextstrain/pathogen-repo-guide/tree/e3bfb52c8155058a3d48592f4268a7382bf3e12a The `ingest/vendored` subdirectory is not copied over since that folder should be added with `git-subrepo`. Future commits will change this to work with lassa data.
…/vendored subrepo: subdir: "ingest/vendored" merged: "c94d78d" upstream: origin: "https://github.com/nextstrain/ingest" branch: "main" commit: "c94d78d" git-subrepo: version: "0.4.6" origin: "https://github.com/ingydotnet/git-subrepo" commit: "110b9eb"
Add a top level nextstrain-pathogen.yaml file to enable nextstrain build from subdirectories. See https://github.com/nextstrain/cli/releases/tag/8.2.0
* https://github.com/nextstrain/dengue/blob/1a9ada3fb0b5a2048ab31769ea0585b0247ebcc8/.github/workflows/ingest.yaml Subsequent commits will modify this for lassa
Nextstrain pathogen repositories should be standardized include `.gitattributes` to force line endings to be LF. We've run into issues in the past with Windows users running into workflow errors because of Windows line endings (CRLF): nextstrain/mpox@def0a71 nextstrain/seasonal-flu@202263a We are letting Git determine if a file is text or binary to avoid corrupting binary files as alluded to by @jameshadfield in review ¹ and suggested by @tsibley in a separate PR.² ¹ #37 (comment) ² nextstrain/mpox#47 (comment)
genehack
approved these changes
Jul 11, 2024
Co-authored-by: John SJ Anderson <[email protected]>
joverlee521
reviewed
Jul 18, 2024
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| workflow_dispatch: | ||
| inputs: | ||
| image: | ||
| description: 'Specific container image to use for ingest workflow (will override the default of "nextstrain build")' | ||
| required: false | ||
| type: string | ||
| trial_name: | ||
| description: | | ||
| Trial name for outputs. | ||
| If not set, outputs will overwrite files at s3://nextstrain-data/files/workflows/lassa/ | ||
| If set, outputs will be uploaded to s3://nextstrain-data/files/workflows/lassa/trials/<trial_name>/ | ||
| required: false | ||
| type: string |
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Copying my comments from rabies because I heard @j23414 mention lassa automation in the priorities meeting
Noting that the this GH Action workflow will error out until rabies is added to the nextstrain/infra repo. See docs for automation.
I want to be explicitly clear here that this workflow does not have an automated schedule. Zika's automated workflow (ingest-to-phylogenetic) calls on the ingest workflow and phylogenetic workflow. Once the phylogenetic workflow is set up in this repo, they can be connected the same way.
Not asking for any changes in this PR, just wanted to make sure we're all on the same page 😄
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Adding lassa to supported pathogen repos in nextstrain/infra#26
joverlee521
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Prompted by nextstrain/lassa#6 which includes the addition of a GH Action workflow that uses pathogen-repo-build workflow.
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Description of proposed changes
Add ingest folder from pathogen-repo-guide and make lassa-specific modifications, following these steps:
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