Reconnect custom parameters

nextstrain · Nov 28, 2024 · 5c8abf1 · 5c8abf1
1 parent 84060d0
commit 5c8abf1
Showing 1 changed file with 3 additions and 4 deletions.
diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk
@@ -82,10 +82,10 @@ rule filter:
             --min-length {params.min_length} \
             --query "{params.query}" \
             --output {output.sequences} \
-            
+            {params.custom_params} \
             2>&1 | tee {log}
         """
-#{params.custom_params} \
+
 rule download_alignment:
     """
     Download the manually fixed GPC alignment that maintains codon alignment
@@ -209,5 +209,4 @@ rule filter_gpc:
             --output {output.sequences} \
             {params.custom_params} \
             2>&1 | tee {log}
-        """
-        #{params.custom_params} \
+        """