Merge pull request #34: Switch to augur curate titlecase and `forma…

…t-dates` subcommands
nextstrain · Sep 15, 2023 · c07627e · c07627e
2 parents 29b1c29 + eb7af54
commit c07627e
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diff --git a/ingest/bin/transform-date-fields b/ingest/bin/transform-date-fields
diff --git a/ingest/bin/transform-string-fields b/ingest/bin/transform-string-fields
diff --git a/ingest/workflow/snakemake_rules/transform.smk b/ingest/workflow/snakemake_rules/transform.smk
@@ -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} \