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Properly handle CSV-like TSVs #23

Closed
Tracked by #1566
joverlee521 opened this issue Dec 6, 2024 · 0 comments · Fixed by #25
Closed
Tracked by #1566

Properly handle CSV-like TSVs #23

joverlee521 opened this issue Dec 6, 2024 · 0 comments · Fixed by #25
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@genehack

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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 18, 2024
genehack added a commit that referenced this issue Dec 18, 2024
@genehack
Add "clean" rules to ingest/phylogenetic Snakefiles [#23]
8ecedff 
This facilitates making sure you're starting with a clean slate when
updating builds.
genehack added a commit that referenced this issue Dec 18, 2024
@genehack
Standardize csvtk and tk-utils usage [#23]
948779c 
* Wrap tsv-utils usage in `csv2tk --csv-delim $'\t'` /
  `csvtk fix-quotes --tabs`
* Remove `csvtk fix-quotes` at start of pipeline in
  "format_ncbi_dataset_report" rule
* Remove '-l' flag in "format_ncbi_dataset_report" rule
@genehack genehack mentioned this issue Dec 18, 2024
Merged
1 task
genehack added a commit that referenced this issue Dec 19, 2024
@genehack
Add "clean" rules to ingest/phylogenetic Snakefiles [#23]
a08660b 
This facilitates making sure you're starting with a clean slate when
updating builds.
genehack added a commit that referenced this issue Dec 19, 2024
@genehack
Standardize csvtk and tk-utils usage [#23]
eb3b0a5 
* Wrap tsv-utils usage in `csv2tk --csv-delim $'\t'` /
  `csvtk fix-quotes --tabs`
* Remove `csvtk fix-quotes` at start of pipeline in
  "format_ncbi_dataset_report" rule
* Remove '-l' flag in "format_ncbi_dataset_report" rule
genehack added a commit that referenced this issue Dec 19, 2024
@genehack
r-quote all shell command strings [#23]
e74b937
genehack added a commit that referenced this issue Dec 20, 2024
@genehack
Standardize csvtk and tk-utils usage [#23]
3c677e7 
* Update "subset_curated_metadata_columns" rule:
  * Swap `tsv-select` for `csvtk cut`

* Update "format_ncbi_dataset_report" rule:
  * Remove '-l' flag from `csvtk add-header`
  * Remove `csvtk del-quotes | tsv-select` at end of pipeline; instead
    extend `csvtk mutate` to handle field re-arrangement
genehack added a commit that referenced this issue Dec 20, 2024
@genehack
r-quote all shell command strings [#23]
fadaaef
genehack added a commit that referenced this issue Dec 20, 2024
@genehack
Merge pull request #25 from nextstrain/tsv-best-practices-23
638fa37 
TSV best practices #23
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TSV best practices #23 nextstrain/oropouche
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@genehack @joverlee521