Provide a no-curation option for NCBI Ingest #30
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enhancement
New feature or request
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I'm not sure we would need custom rules here... It should be enough to document the NCBI Datasets output target |
joverlee521
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Provides an easy way for first time users to get the uncurated metadata from NCBI Datasets commands by running the ingest workflow with the specified target `data/ncbi_dataset_report.tsv`. Afterwards, users can easily remove fields that are not needed as part the workflow to reduce the file size and save space. Prompted by @jameshadfield in review of the tutorial¹ and resolves #30. ¹ nextstrain/docs.nextstrain.org#195 (comment)
joverlee521
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Mar 29, 2024
Provides an easy way for first time users to get the full uncurated metadata from NCBI Datasets commands by running the ingest workflow with the specified target `dump_ncbi_dataset_report`. They can then inspect and explore the raw data to determine if they want to configure the workflow to use additional fields from NCBI. The rule is added to `fetch_from_ncbi.smk` to make it easy to run without additional configs. Note that it is not run as part of the default workflow and only intended to be used as a specified target. Prompted by @jameshadfield in review of the tutorial¹ and resolves #30. ¹ nextstrain/docs.nextstrain.org#195 (comment) Co-authored-by: James Hadfield <hadfield.james@gmail.com>
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Context
Inspired by a review comment of the measles/add-ingest pull request, propose an optional rule for skipping (or bypassing) curation steps to produce raw outcomes. These outcomes can then guide the selection of specific curation steps or metadata field transformations.
This idea is loosely connected to the effort of standardizing NCBI field transformations, as discussed in #20.
Description
Allow users to initiate ingest to produce an uncurated
metadata.tsvfile, from which they can compare against the curatedmetadata.tsvfile. Users can then decide which curation steps to opt-in for or choose to use our defaults.Examples
Possible solution
One potential approach includes utilizing the "custom_rules" config in the Snakefile. Users can then import "no-curate" rules that take data/ncbi.ndjson , pass it through augur curate passthru , and generate an uncurated
metadata.tsvfile.The text was updated successfully, but these errors were encountered: