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Properly handle CSV-like TSVs #27

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Tracked by #1566
joverlee521 opened this issue Dec 6, 2024 · 0 comments · May be fixed by #31
Open
Tracked by #1566

Properly handle CSV-like TSVs #27

joverlee521 opened this issue Dec 6, 2024 · 0 comments · May be fixed by #31
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Parent issue: nextstrain/augur#1566

Audit handling of TSVs in the repo to ensure that we are properly manipulating CSV-like TSVs.
See Nextstrain Data formats docs for guidelines.
@joverlee521 joverlee521 mentioned this issue Dec 6, 2024
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@genehack genehack self-assigned this Dec 9, 2024
genehack added a commit that referenced this issue Dec 20, 2024
@genehack
Align with TSV best practices [#27]
aee697a 
* in "subset_metadata" rule:
  * use `csvtk cut` instead of `tsv-select`; avoids need to filter
    input and output through `csvtk`
* in "format_ncbi_dataset_report" rule:
  * extend `csvtk mutate` command to also handle field re-arrangement
@genehack genehack linked a pull request Dec 20, 2024 that will close this issue
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Align with TSV best practices [#27] nextstrain/yellow-fever
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@genehack @joverlee521