fixup! Use only the 21L sequence from references

nextstrain · Sep 30, 2024 · 229eebb · 229eebb
1 parent 97a3309
commit 229eebb
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/nextstrain_profiles/nextstrain-gisaid-21L/prefilter.smk b/nextstrain_profiles/nextstrain-gisaid-21L/prefilter.smk
@@ -91,8 +91,10 @@ rule gisaid_21L_aligned:
         r"""
         exec 2> {log:q}
 
+        echo "21L" > reference_ids.txt
+
         < {input.references:q} \
-          seqkit grep --by-name -f <(echo "21L") \
+          seqkit grep --by-name -f reference_ids.txt \
         | zstd \
         > {output.aligned}
 
@@ -101,4 +103,6 @@ rule gisaid_21L_aligned:
         | seqkit grep --by-name -f {input.strains:q} \
         | zstd -T$(({threads} - 2)) \
         >> {output.aligned:q}
+
+        rm reference_ids.txt
         """