From 36eb076820f925f42755af205f4a4a6c6804ed03 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontushojer@gmail.com>
Date: Wed, 29 Jul 2026 11:02:28 +0200
Subject: [PATCH 1/2] Fix 'multiqc_title' param modifying the output directory
 structure, breaking the report index section
 ([#261](https://github.com/nf-core/seqinspector/issues/261))

---
 CHANGELOG.md              | 2 ++
 assets/multiqc_config.yml | 6 ++++++
 2 files changed, 8 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f86e7a8b..8f632895 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#264](https://github.com/nf-core/seqinspector/pull/264) Fix `--multiqc_title` modifying the output directory structure, breaking the report index section ([#261](https://github.com/nf-core/seqinspector/issues/261))
+
 ### `Changed`
 
 - [#259](https://github.com/nf-core/seqinspector/pull/259) Back to dev
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index b219abfd..18d4277b 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -14,6 +14,12 @@ report_section_order:
 
 export_plots: true
 
+# Set static output file names for the report, data and plots directories so these
+# are not changed when "--multiqc_title" is specified, required for index section to work properly
+output_fn_name: "multiqc_report.html"
+data_dir_name: "multiqc_data"
+plots_dir_name: "multiqc_plots"
+
 disable_version_detection: true
 
 fn_clean_trim:

From 4e4231fdbbaf1f69b5ecd3cfe820d6747f438991 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Pontus=20H=C3=B6jer?= <pontus.hojer@scilifelab.se>
Date: Wed, 29 Jul 2026 11:59:11 +0200
Subject: [PATCH 2/2] update parameter desc

---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 08cea605..e6a77c8f 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -46,7 +46,7 @@
                 },
                 "multiqc_title": {
                     "type": "string",
-                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
+                    "description": "MultiQC report title. Printed as page header.",
                     "fa_icon": "fas fa-file-signature"
                 },
                 "tools": {