--trim to gofasta cmd

cov-lineages · Apr 29, 2021 · 4fc674f · 4fc674f
1 parent 4263545
commit 4fc674f
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/pangolin/scripts/pangolearn.smk b/pangolin/scripts/pangolearn.smk
@@ -50,6 +50,7 @@ rule align_to_reference:
             --reference {input.reference:q} \
             --trimstart {params.trim_start} \
             --trimend {params.trim_end} \
+            --trim \
             --pad > {output.fasta:q}
         """