Fix: mirdeep2 mapper statistics are emitted to standard error

OpenOmics · Aug 8, 2023 · 6c61933 · 6c61933
1 parent 4d18f49
commit 6c61933
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/workflow/rules/align.smk b/workflow/rules/align.smk
@@ -60,7 +60,7 @@ rule mirdeep2_mapper:
         -t {output.arf} \\
         -v \\
         -o {threads} \\
-    > {output.map_log}
+    > {output.map_log} 2>&1
 
     # Extract mapper statistics
     paste \\
@@ -114,4 +114,5 @@ rule mirdeep2_gather_mapper_statistics:
         awk 'NR=="2" {{print}}' "${{f}}" \\
         >> {output.map_tsv}
         i=$((i + 1))
+    done
     """