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cgoina
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Nov 12, 2025
| migrate = "alembic upgrade head" | ||
| migrate-create = "alembic revision --autogenerate" | ||
| migrate = { cmd = "alembic upgrade head", cwd = "fileglancer" } | ||
| migrate-create = { cmd = "alembic revision --autogenerate", cwd = "fileglancer" } |
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These changes are actually needed for these tasks to work. I also updated development docs with a section for database changes.
cgoina
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Nov 12, 2025
| ignore = ["W002"] | ||
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| [tool.pixi.project] | ||
| [tool.pixi.workspace] |
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I think @neomorphic was already asking to make this change
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@krokicki @neomorphic @allison-truhlar
This is related to https://app.clickup.com/t/86ad02fne story for starting the discussion about task plugins.
So far there is a mechanism to register these plugins with the python setuptools entry points and there's a generic task that could potentially run any nextflow workflow.
The parameters returned are based on the metadata from argparse parameters and since it is not tied to a specific pipeline it does not know how to get the parameters that could be defined in the pipeline's nextflow_schema.
The exposed endpoints are also very limited and there's no UI - just very few apis related to getting available tasks, the parameters and starting a new tasks.
The corresponding model is defined but nothing is persisted in the db yet. Getting the task status will also depend on that.