From 9ba657984b80fed2cec24d0f8d93c64c5d797058 Mon Sep 17 00:00:00 2001
From: torossee <toon.rosseel@ugent.be>
Date: Wed, 1 Oct 2025 14:25:19 +0200
Subject: [PATCH 1/2] process_beds: optimize for HyperCap data

---
 CHANGELOG.md                       | 1 +
 conf/hypercap.config               | 5 +++++
 modules/local/process_beds/main.nf | 1 +
 3 files changed, 7 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index bf8b6a95..801befcc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## Changes
 
 1. Renamed the `tbi` samplesheet field to `gtbi` to make it more clear that this is the index of the GVCF file.
+2. Process_bed module: add sorting step + git HyperCap profile more memory.
 
 ## v1.11.0 - Generous Ghent - [Sept 1 2025]
 
diff --git a/conf/hypercap.config b/conf/hypercap.config
index 9ce274d8..e59fc600 100644
--- a/conf/hypercap.config
+++ b/conf/hypercap.config
@@ -9,3 +9,8 @@ params {
     scatter_count       = 5
     only_pass           = true
 }
+process {
+    withName: PROCESS_BEDS {
+        memory = 64.GB
+    }
+}
diff --git a/modules/local/process_beds/main.nf b/modules/local/process_beds/main.nf
index ae633b76..633db241 100644
--- a/modules/local/process_beds/main.nf
+++ b/modules/local/process_beds/main.nf
@@ -28,6 +28,7 @@ process PROCESS_BEDS {
     ${unzip} ${bed} \\
         | grep ${args} \\
         | bedtools merge ${args2} \\
+        | bedtools sort -faidx ${fai} \\
         ${intersect} \\
         > ${prefix}.bed
 

From 0a8f25dec7603a0fbe59ee358391ae188fec65c0 Mon Sep 17 00:00:00 2001
From: torossee <toon.rosseel@ugent.be>
Date: Wed, 1 Oct 2025 14:29:16 +0200
Subject: [PATCH 2/2] fix

---
 modules/local/process_beds/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/process_beds/main.nf b/modules/local/process_beds/main.nf
index 633db241..22e174f8 100644
--- a/modules/local/process_beds/main.nf
+++ b/modules/local/process_beds/main.nf
@@ -27,8 +27,8 @@ process PROCESS_BEDS {
     """
     ${unzip} ${bed} \\
         | grep ${args} \\
-        | bedtools merge ${args2} \\
         | bedtools sort -faidx ${fai} \\
+        | bedtools merge ${args2} \\
         ${intersect} \\
         > ${prefix}.bed