From 974edd968230231d77710d5f5aebe864c2771ff1 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Fri, 23 Aug 2024 09:12:45 -0400
Subject: [PATCH 1/2] fix: manorm used tagalign2 twice

fixes #197
---
 modules/local/manorm/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/manorm/main.nf b/modules/local/manorm/main.nf
index e562e623..d25e108c 100644
--- a/modules/local/manorm/main.nf
+++ b/modules/local/manorm/main.nf
@@ -18,7 +18,7 @@ process MANORM_PAIRWISE {
     manorm \\
         --p1 ${peak1} \\
         --p2 ${peak2} \\
-        --r1 ${tagalign2} \\
+        --r1 ${tagalign1} \\
         --r2 ${tagalign2} \\
         --s1 ${meta1.fraglen} \\
         --s2 ${meta2.fraglen} \\

From 7071bc29a7ebba49f38adbc0476e2b06441a114d Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Mon, 26 Aug 2024 09:01:04 -0400
Subject: [PATCH 2/2] chore: update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5da94fcf..a0bd657b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,7 @@
 - In the biowulf config profile, switch variable $SLURM_JOBID to $SLURM_JOB_ID. (@kelly-sovacool)
 - Increase resource allocations for chipseeker and deeptools. (#192, @slsevilla)
 - Check the validity of the contrastsheet earlier on in the workflow. (#192, @slsevilla; #200, @kelly-sovacool)
+- Fix bug where `manorm` was using R1 twice instead of R1 and R2. (#206, @kelly-sovacool)
 
 ### Misc