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Ingest nextclade updates #54
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I guess I've never tested running this path of the ingest workflow. Error showed up when I tried to run the workflow with the Nextclade config. ``` nextstrain build ingest results/metadata.tsv --config ncbi_taxon_id='64320' --configfile defaults/nextclade_config.yaml --forceall -n Config file defaults/config.yaml is extended by additional config specified via the command line. Building DAG of jobs... MissingInputException in rule join_metadata_and_nextclade in file /nextstrain/build/ingest/rules/nextclade.smk, line 64: Missing input files for rule join_metadata_and_nextclade: output: results/metadata.tsv affected files: config/nextclade_field_map.tsv ```
This was originally copied from mpox and `lineage` is a very mpox specific field that is not usually included in the Nextclade output TSV.
This was written before Nextclade v3 was officially released. Nextclade v3 been out for >6 months now and all new Nextclade datasets are expected to be v3.
I was running into a weird error when testing this PR with mpox:
Turns out the root error is coming from
I'm going to drop dc9ac25 for now and follow up in a separate change -> see |
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@joverlee521 Oh no, so fix-quotes, which is a workaround for csvtk's lack of TSV support has its own quirks? This strengthens my opinion that we should just never use csvtk for TSVs 🙃 I see that this is exactly what you're doing in #55 |
Description of proposed changes
Various small fixes for the Nextclade rules of the ingest workflow.
See commits for details.
Related issue(s)
Resolves #47
Related to https://github.com/nextstrain/private/issues/97
Checklist