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ingest: GenBank accession should not include version number #39

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joverlee521 opened this issue Apr 12, 2024 · 1 comment · Fixed by #40
Closed

ingest: GenBank accession should not include version number #39

joverlee521 opened this issue Apr 12, 2024 · 1 comment · Fixed by #40
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enhancement New feature or request

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@joverlee521
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Originally brought up in nextstrain/measles#24, but we most likely don't want to include version number in all future Nextstrain pathogens.

Currently the version is stripped and added as a new column in

We can add similar csvtk and tsv-select commands to

pathogen-repo-guide/ingest/rules/fetch_from_ncbi.smk

Lines 95 to 100 in 0f799d7

dataformat tsv virus-genome \
--package {input.dataset_package} \
--fields {params.ncbi_datasets_fields:q} \
--elide-header \
| csvtk add-header -t -l -n {params.ncbi_datasets_fields:q} \
> {output.ncbi_dataset_tsv}

@joverlee521 joverlee521 added the enhancement New feature or request label Apr 12, 2024
@joverlee521
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Relevant to discussion of what should standardized metadata fields be in #20

joverlee521 added a commit that referenced this issue Apr 17, 2024
@joverlee521
ingest: Create new accession field without version
ceb7fbc 
Resolves #39

Create a new accession field without the version number so that
annotations do not need to be updated when the version number is updated.
@joverlee521 joverlee521 mentioned this issue Apr 17, 2024
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ingest: Create new accession field without version nextstrain/pathogen-repo-guide
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