fix: makes the compress rule more generic

Co-authored-by: Thomas Sibley <tom@zulutango.org>
nextstrain · Mar 28, 2023 · c932c00 · c932c00
1 parent a3269e2
commit c932c00
Showing 1 changed file with 7 additions and 8 deletions.
diff --git a/ingest/workflow/snakemake_rules/transform.smk b/ingest/workflow/snakemake_rules/transform.smk
@@ -107,25 +107,24 @@ rule transform:
                 --sequence-field {params.sequence_field} ) 2>> {log}
         """
 
+
 rule post_process_metadata:
     input:
         metadata="data/raw_metadata_{serotype}.tsv",
     output:
         metadata="data/metadata_{serotype}.tsv",
     shell:
-       """
+        """
        ./bin/post_process_metadata.py --metadata {input.metadata} --outfile {output.metadata}
        """
 
+
 rule compress:
     input:
-        sequences="data/sequences_{serotype}.fasta",
-        metadata="data/metadata_{serotype}.tsv",
+        file="{a_file}",
     output:
-        sequences="data/sequences_{serotype}.fasta.zst",
-        metadata="data/metadata_{serotype}.tsv.zst",
+        file_compressed="{a_file}.zst",
     shell:
         """
-        zstd -T0 -o {output.sequences} {input.sequences}
-        zstd -T0 -o {output.metadata} {input.metadata}
-        """
+        zstd -T0 -o {output.file_compressed} {input.file}
+        """