Use ingest/scripts to match phylogenetic/scripts #66

nextstrain · Jul 8, 2024 · e05770b · e05770b
2 parents 23263aa + 8c71cda
commit e05770b
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Showing 5 changed files with 2 additions and 13 deletions.
diff --git a/ingest/rules/curate.smk b/ingest/rules/curate.smk
@@ -90,11 +90,11 @@ rule curate:
                 --default-value {params.authors_default_value} \
             | ./vendored/apply-geolocation-rules \
                 --geolocation-rules {input.all_geolocation_rules} \
-            | ./bin/fix-zika-strain-names.py \
+            | ./scripts/fix-zika-strain-names.py \
             | ./vendored/merge-user-metadata \
                 --annotations {input.annotations} \
                 --id-field {params.annotations_id} \
-            | ./bin/ndjson-to-tsv-and-fasta \
+            | ./scripts/ndjson-to-tsv-and-fasta \
                 --metadata-columns {params.metadata_columns} \
                 --metadata {output.metadata} \
                 --fasta {output.sequences} \

diff --git a/ingest/bin/fasta-to-ndjson → ingest/scripts/fasta-to-ndjson b/ingest/bin/fasta-to-ndjson → ingest/scripts/fasta-to-ndjson
diff --git a/ingest/bin/fix-zika-strain-names.py → ingest/scripts/fix-zika-strain-names.py b/ingest/bin/fix-zika-strain-names.py → ingest/scripts/fix-zika-strain-names.py
diff --git a/ingest/bin/ndjson-to-tsv-and-fasta → ingest/scripts/ndjson-to-tsv-and-fasta b/ingest/bin/ndjson-to-tsv-and-fasta → ingest/scripts/ndjson-to-tsv-and-fasta
diff --git a/phylogenetic/scripts/check-countries-have-colors.sh b/phylogenetic/scripts/check-countries-have-colors.sh