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Switch to augur curate titlecase and format-dates subcommands #34

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merged 2 commits into from
Sep 15, 2023
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Switch to augur curate titlecase and format-dates subcommands #34

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19ceb13
Switch to augur curate format-dates
j23414 Jul 28, 2023
eb7af54
Switch to augur curate titlecase
j23414 Aug 3, 2023
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154 changes: 0 additions & 154 deletions ingest/bin/transform-date-fields
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84 changes: 0 additions & 84 deletions ingest/bin/transform-string-fields
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4 changes: 2 additions & 2 deletions ingest/workflow/snakemake_rules/transform.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -71,11 +71,11 @@ rule transform:
| ./bin/transform-strain-names \
--strain-regex {params.strain_regex} \
--backup-fields {params.strain_backup_fields} \
| ./bin/transform-date-fields \
| augur curate format-dates \
--date-fields {params.date_fields} \
--expected-date-formats {params.expected_date_formats} \
| ./vendored/transform-genbank-location \
| ./bin/transform-string-fields \
| augur curate titlecase \
--titlecase-fields {params.titlecase_fields} \
--articles {params.articles} \
--abbreviations {params.abbreviations} \
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