From 42e4d79a3acbb321d64390364fcd44fa0bc72915 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=96zlem=20Muslu?= <ozlemmuslu@gmail.com>
Date: Tue, 4 Feb 2025 14:34:20 +0100
Subject: [PATCH 1/3] Update strelka2.nf

Parameterize mempry and cpus
---
 modules/strelka2.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/strelka2.nf b/modules/strelka2.nf
index 2ea17b6..49a566c 100644
--- a/modules/strelka2.nf
+++ b/modules/strelka2.nf
@@ -32,8 +32,8 @@ process STRELKA2 {
 }
 
 process CONCAT_FILES {
-    cpus 1
-    memory '4g'
+    cpus "${params.cpus}"
+    memory "${params.memory}"
     publishDir "${params.output}/${name}", mode: 'copy'
     tag "${name}"
 

From f86e95b8b43358cdbe7a9cded29483a22cd5fc50 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=96zlem=20Muslu?= <ozlemmuslu@gmail.com>
Date: Tue, 4 Feb 2025 14:34:47 +0100
Subject: [PATCH 2/3] Parameterize cpus and memory

---
 modules/merge_replicates.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/merge_replicates.nf b/modules/merge_replicates.nf
index 490c00b..ec6b4b9 100644
--- a/modules/merge_replicates.nf
+++ b/modules/merge_replicates.nf
@@ -2,8 +2,8 @@
 
 process MERGE_REPLICATES {
     tag "$name"
-    cpus 1
-    memory '4g'
+    cpus "${params.cpus}"
+    memory "${params.memory}"
 
     conda (params.enable_conda ? 'conda-forge::libgcc-ng=10.3.0 conda-forge::gsl=2.7 bioconda::samtools=1.15.1' : null)
 
@@ -37,4 +37,4 @@ process MERGE_REPLICATES {
     ${normal_merge_cmd}
     samtools index ${name}.normal.bam
     """
-}
\ No newline at end of file
+}

From 2cc71ce9e0531cd6ebae2cacc8126b9477e80ed5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=C3=96zlem=20Muslu?= <ozlemmuslu@gmail.com>
Date: Tue, 4 Feb 2025 14:35:31 +0100
Subject: [PATCH 3/3] Bump version

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index ecd56c5..f20276c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -34,7 +34,7 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
 
 cleanup = true
 
-VERSION = '0.2.2'
+VERSION = '0.2.3'
 DOI = 'doi'
 
 manifest {