Moved duckdb files into a separate directory root.

src/snakefiles/duckdb.snakefile

@@ -7,7 +7,7 @@ import os
 # Write all compendia files to DuckDB and Parquet, then create `babel_outputs/duckdb/compendia_done` to signal that we're done.
 rule export_all_compendia_to_duckdb:
     input:
-        nodes_files=expand("{od}/duckdb/parquet/filename={fn}/compendium.duckdb",
+        nodes_files=expand("{od}/duckdb/duckdbs/filename={fn}/compendium.duckdb",
             od=config['output_directory'],
             fn=map(lambda fn: os.path.splitext(fn)[0], get_all_compendia(config))
         )
@@ -30,7 +30,7 @@ rule export_compendia_to_duckdb:
 # Write all synonyms files to Parquet via DuckDB, then create `babel_outputs/duckdb/synonyms_done` to signal that we're done.
 rule export_all_synonyms_to_duckdb:
     input:
-        sapbert_training_file=expand("{od}/duckdb/parquet/filename={fn}/synonyms.duckdb",
+        sapbert_training_file=expand("{od}/duckdb/duckdbs/filename={fn}/synonyms.duckdb",
             od=config['output_directory'],
             fn=map(lambda fn: os.path.splitext(fn)[0], get_all_synonyms_with_drugchemicalconflated(config))
         )
@@ -45,7 +45,7 @@ rule export_synonyms_to_duckdb:
     input:
         synonyms_file=config['output_directory'] + "/synonyms/{filename}.txt",
     output:
-        duckdb_filename=config['output_directory'] + "/duckdb/parquet/filename={filename}/synonyms.duckdb"
+        duckdb_filename=config['output_directory'] + "/duckdb/duckdbs/filename={filename}/synonyms.duckdb"
     run:
         duckdb_exporters.export_synonyms_to_parquet(input.synonyms_file, output.duckdb_filename)