From 6c619337255de1ce1ed25a7130f03c6cc0d2c6b6 Mon Sep 17 00:00:00 2001
From: skchronicles <kuhnsa3@gmail.com>
Date: Tue, 8 Aug 2023 11:35:43 -0400
Subject: [PATCH] Fix: mirdeep2 mapper statistics are emitted to standard error

---
 workflow/rules/align.smk | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/workflow/rules/align.smk b/workflow/rules/align.smk
index 982d409..cae060b 100644
--- 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
     """