From 0d337393f455c8b5cc8256cf7e66aac477988e11 Mon Sep 17 00:00:00 2001
From: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>
Date: Thu, 28 Nov 2024 10:08:28 +0100
Subject: [PATCH 1/2] Move modules config import after base.config

---
 nf_core/pipeline-template/nextflow.config | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 6970d0518..a9aa9c553 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -76,6 +76,11 @@ params {
 includeConfig 'conf/base.config'
 {%- else %}
 
+{% if modules -%}
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
+{%- endif %}
+
 process {
     // TODO nf-core: Check the defaults for all processes
     cpus   = { 1    * task.attempt }
@@ -316,8 +321,3 @@ validation {
     }{% endif %}
 }
 {%- endif %}
-
-{% if modules -%}
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
-{%- endif %}

From c8f22cfe7f7cd97718741949474304bb99cb8e6f Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Thu, 28 Nov 2024 16:24:26 +0100
Subject: [PATCH 2/2] Update CHANGELOG.md

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 36ea94084..f418dc0af 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@
 - Add resource limits to Gitpod profile([#3255](https://github.com/nf-core/tools/pull/3255))
 - Fix a typo ([#3268](https://github.com/nf-core/tools/pull/3268))
 - Remove `def` from `nextflow.config` and add `trace_report_suffix` param ([#3296](https://github.com/nf-core/tools/pull/3296))
+- Move `includeConfig 'conf/modules.config'` next to `includeConfig 'conf/base.config'` to not overwrite tests profiles configurations ([#3301](https://github.com/nf-core/tools/pull/3301))
 
 ### Download