From ed0a58f407b6a898755d71e0fd92611140e13498 Mon Sep 17 00:00:00 2001
From: Maxime U Garcia <max.u.garcia@gmail.com>
Date: Wed, 30 Aug 2023 15:33:32 +0200
Subject: [PATCH 1/4] Update multiqc_config.yml

Change URL to the release tag
---
 nf_core/pipeline-template/assets/multiqc_config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/assets/multiqc_config.yml b/nf_core/pipeline-template/assets/multiqc_config.yml
index 9423ee53f7..590f3fcdf6 100644
--- a/nf_core/pipeline-template/assets/multiqc_config.yml
+++ b/nf_core/pipeline-template/assets/multiqc_config.yml
@@ -4,7 +4,7 @@ report_comment: >
   analysis pipeline.{% if branded %} For information about how to interpret these results, please see the
   <a href="https://nf-co.re/{{ short_name }}/dev/docs/output" target="_blank">documentation</a>.{% endif %}
   {%- else %}
-  This report has been generated by the <a href="https://github.com/{{ name }}/tree/{{ version }}" target="_blank">{{ name }}</a>
+  This report has been generated by the <a href="https://github.com/{{ name }}/releases/tag/{{ version}}" target="_blank">{{ name }}</a>
   analysis pipeline.{% if branded %} For information about how to interpret these results, please see the
   <a href="https://nf-co.re/{{ short_name }}/{{ version }}/docs/output" target="_blank">documentation</a>.{% endif %}
   {% endif %}

From 0209233d43f909df43f5570066e1726453e966f7 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 19 Sep 2023 10:47:10 +0200
Subject: [PATCH 2/4] update linting of multiqc_config.yml

---
 nf_core/lint/multiqc_config.py                      | 2 +-
 nf_core/pipeline-template/assets/multiqc_config.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/nf_core/lint/multiqc_config.py b/nf_core/lint/multiqc_config.py
index 4877b41194..a1b831ae2d 100644
--- a/nf_core/lint/multiqc_config.py
+++ b/nf_core/lint/multiqc_config.py
@@ -76,7 +76,7 @@ def multiqc_config(self):
             if "report_comment" not in mqc_yml:
                 raise AssertionError()
             if mqc_yml["report_comment"].strip() != (
-                f'This report has been generated by the <a href="https://github.com/nf-core/{self.pipeline_name}/tree/{version}" '
+                f'This report has been generated by the <a href="https://github.com/nf-core/{self.pipeline_name}/releases/tag/{version}" '
                 f'target="_blank">nf-core/{self.pipeline_name}</a> analysis pipeline. For information about how to '
                 f'interpret these results, please see the <a href="https://nf-co.re/{self.pipeline_name}/{version}/docs/output" '
                 'target="_blank">documentation</a>.'
diff --git a/nf_core/pipeline-template/assets/multiqc_config.yml b/nf_core/pipeline-template/assets/multiqc_config.yml
index 590f3fcdf6..39943ffe49 100644
--- a/nf_core/pipeline-template/assets/multiqc_config.yml
+++ b/nf_core/pipeline-template/assets/multiqc_config.yml
@@ -4,7 +4,7 @@ report_comment: >
   analysis pipeline.{% if branded %} For information about how to interpret these results, please see the
   <a href="https://nf-co.re/{{ short_name }}/dev/docs/output" target="_blank">documentation</a>.{% endif %}
   {%- else %}
-  This report has been generated by the <a href="https://github.com/{{ name }}/releases/tag/{{ version}}" target="_blank">{{ name }}</a>
+  This report has been generated by the <a href="https://github.com/{{ name }}/releases/tag/{{ version }}" target="_blank">{{ name }}</a>
   analysis pipeline.{% if branded %} For information about how to interpret these results, please see the
   <a href="https://nf-co.re/{{ short_name }}/{{ version }}/docs/output" target="_blank">documentation</a>.{% endif %}
   {% endif %}

From c0f8948febfd674097d48a305c5635423250b60e Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 19 Sep 2023 10:48:30 +0200
Subject: [PATCH 3/4] update changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4c6cfc1fa9..a02b1106d0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,7 +4,7 @@
 
 ### Template
 
-- Fix links in `multiqc_config.yml` ([#2372](https://github.com/nf-core/tools/pull/2372))
+- Fix links in `multiqc_config.yml` ([#2372](https://github.com/nf-core/tools/pull/2372) and [#2412](https://github.com/nf-core/tools/pull/2412))
 - Remove default false from nextflow_schema.json ([#2376](https://github.com/nf-core/tools/pull/2376))
 - Add module MULTIQC to modules.config ([#2377](https://github.com/nf-core/tools/pull/2377))
 - Add GitHub workflow for automated release announcements ([#2382](https://github.com/nf-core/tools/pull/2382))

From 6b20a81c31c11c19ab62b1764dbcac9470ecc4f8 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Tue, 19 Sep 2023 14:45:38 +0200
Subject: [PATCH 4/4] Update multiqc_config.yml dev link

---
 nf_core/pipeline-template/assets/multiqc_config.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf_core/pipeline-template/assets/multiqc_config.yml b/nf_core/pipeline-template/assets/multiqc_config.yml
index 39943ffe49..9ab59067a1 100644
--- a/nf_core/pipeline-template/assets/multiqc_config.yml
+++ b/nf_core/pipeline-template/assets/multiqc_config.yml
@@ -1,6 +1,6 @@
 report_comment: >
   {% if 'dev' in version -%}
-  This report has been generated by the <a href="https://github.com/{{ name }}/tree/dev" target="_blank">{{ name }}</a>
+  This report has been generated by the <a href="https://github.com/{{ name }}/releases/tag/dev" target="_blank">{{ name }}</a>
   analysis pipeline.{% if branded %} For information about how to interpret these results, please see the
   <a href="https://nf-co.re/{{ short_name }}/dev/docs/output" target="_blank">documentation</a>.{% endif %}
   {%- else %}