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ingest: Add example build-config/ci/config.yaml #71

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genehack opened this issue Oct 29, 2024 · 1 comment
Closed

ingest: Add example build-config/ci/config.yaml #71

genehack opened this issue Oct 29, 2024 · 1 comment

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@genehack
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genehack commented Oct 29, 2024 •
edited by tsibley
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Snakemake requires at least one top level key in a config file, so including a bogus key here that should not be used anywhere in the Snakemake workflow

More precisely, Snakemake requires a YAML file with a top-level map/dict/object type. It may be empty; keys are not required.

We could avoid the bogus config key above by using flow syntax for a map ({}) instead, e.g.

# TODO: If the ingest workflow ever runs too long, we should figure out a way
# to subset the ingest data. Currently, the CI just runs the default ingest workflow.
{}

The bogus config key also got propagated to measles, rabies, and oropouche, and seems likely to propagate further over time. It'd be nice to avoid, IMO.

Originally posted by @tsibley in 44f27a5
genehack referenced this issue in nextstrain/zika Oct 29, 2024
@joverlee521
ingest: Add CI build config
44f27a5 
The ingest workflow current runs in <1 minute so I figured it'd be nice
to add as an additional check in the GH Action CI workflow.
If the ingest workflow ever runs for too long, we should figure out a
way to subset the ingest data.

The CI build config includes a bogus key because Snakemake requires the
config file to have at least one top level key.

Previous CI run without the bogus key ran into an error¹
```
snakemake.exceptions.WorkflowError: Config file must be given as JSON or YAML with keys at top level.
```

¹ <https://github.com/nextstrain/zika/actions/runs/9948628997/job/27483549394#step:9:17>
@joverlee521 joverlee521 changed the title Change bogus key to empty object ingest: Add example build-config/ci/config.yaml Oct 29, 2024
@joverlee521
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Consolidated with #56

@joverlee521 joverlee521 closed this as not planned Won't fix, can't repro, duplicate, stale Nov 26, 2024
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@genehack @joverlee521