From db40231e96132cb06caa4e6c7c1207117efb25f6 Mon Sep 17 00:00:00 2001
From: Danilo Tatoni <36413174+danilotat@users.noreply.github.com>
Date: Tue, 18 Nov 2025 13:20:57 +0100
Subject: [PATCH] fix: closes ctglab/ctgflow#7

---
 workflow/rules/alignment.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/rules/alignment.smk b/workflow/rules/alignment.smk
index acf2d4f..f566a36 100644
--- a/workflow/rules/alignment.smk
+++ b/workflow/rules/alignment.smk
@@ -11,7 +11,7 @@ rule combine_fqs:
         ),
         r2=lookup(
             query=lambda w: f"patient == '{w.patient}' and sample == '{w.sample_type}' and readgroup == '{w.readgroup}'",
-            cols=["fq1"],
+            cols=["fq2"],
             within=units
         ),
     output: